PROTEINS

From the Current Issue: January 15 2007; 92 (2) [Table of Contents]

Jessica Plati, Natia Tsomaia, Andrea Piserchio, and Dale F. Mierke

Structural Features of Parathyroid Hormone Receptor Coupled to G_S-Protein
Biophys. J. 2007. 92:535-540. [Abstract] [Full Text] [PDF]

Nolan B. Holland, Yoshiyuki Nishimiya, Sakae Tsuda, and Frank D. Sonnichsen

Activity of a Two-Domain Antifreeze Protein Is Not Dependent on Linker Sequence
Biophys. J. 2007. 92:541-546. [Abstract] [Full Text] [PDF]

Mai Suan Li, Maksim Kouza, and Chin-Kun Hu

Refolding upon Force Quench and Pathways of Mechanical and Thermal Unfolding of Ubiquitin
Biophys. J. 2007. 92:547-561. [Abstract] [Full Text] [PDF]

Deepa Bhatt, S. Zoe Fisher, Chingkuang Tu, Robert McKenna, and David N. Silverman

Location of Binding Sites in Small Molecule Rescue of Human Carbonic Anhydrase II
Biophys. J. 2007. 92:562-570. [Abstract] [Full Text] [PDF]

Lucy G. Randles, Ross W. S. Rounsevell, and Jane Clarke

Spectrin Domains Lose Cooperativity in Forced Unfolding
Biophys. J. 2007. 92:571-577. [Abstract] [Full Text] [PDF]

Jing-Tan Su, Sung-Hye Kim, and Yong-Bin Yan

Dissecting the Pretransitional Conformational Changes in Aminoacylase I Thermal Denaturation
Biophys. J. 2007. 92:578-587. [Abstract] [Full Text] [PDF]

From Past Issues:

Sharmistha Sinha and Avadhesha Surolia

Attributes of Glycosylation in the Establishment of the Unfolding Pathway of Soybean Agglutinin
Biophys. J. 2007. 92:208-216. [Abstract] [Full Text] [PDF]

Nathalie Colloc'h, Jana Sopkova-de Oliveira Santos, Pascal Retailleau, Denis Vivares, Francoise Bonnete, Beatrice Langlois d'Estainto, Bernard Gallois, Alain Brisson, Jean-Jacques Risso, Marc Lemaire, Thierry Prange, and Jacques H. Abraini

Protein Crystallography under Xenon and Nitrous Oxide Pressure: Comparison with In Vivo Pharmacology Studies and Implications for the Mechanism of Inhaled Anesthetic Action
Biophys. J. 2007. 92:217-224. [Abstract] [Full Text] [PDF]

Sri Rama Koti Ainavarapu, Jasna Brujic, Hector H. Huang, Arun P. Wiita, Hui Lu, Lewyn Li, Kirstin A. Walther, Mariano Carrion-Vazquez, Hongbin Li, and Julio M. Fernandez

Contour Length and Refolding Rate of a Small Protein Controlled by Engineered Disulfide Bonds
Biophys. J. 2007. 92:225-233. [Abstract] [Full Text] [PDF]

Atul Saluja, Advait V. Badkar, David L. Zeng, Sandeep Nema, and Devendra S. Kalonia

Ultrasonic Storage Modulus as a Novel Parameter for Analyzing Protein-Protein Interactions in High Protein Concentration Solutions: Correlation with Static and Dynamic Light Scattering Measurements
Biophys. J. 2007. 92:234-244. [Abstract] [Full Text] [PDF]

Allan Chris M. Ferreon, Josephine C. Ferreon, D. Wayne Bolen, and Jorg Rosgen

Protein Phase Diagrams II: Nonideal Behavior of Biochemical Reactions in the Presence of Osmolytes
Biophys. J. 2007. 92:245-256. [Abstract] [Full Text] [PDF]

Stina Lindman, Sara Linse, Frans A. A. Mulder, and Ingemar Andre

pK_a Values for Side-Chain Carboxyl Groups of a PGB1 Variant Explain Salt and pH-Dependent Stability
Biophys. J. 2007. 92:257-266. [Abstract] [Full Text] [PDF]

Weichun Pan, Oleg Galkin, Luis Filobelo, Ronald L. Nagel, and Peter G. Vekilov

Metastable Mesoscopic Clusters in Solutions of Sickle-Cell Hemoglobin
Biophys. J. 2007. 92:267-277. [Abstract] [Full Text] [PDF]

Ning Du, Xiang Yang Liu, Janaky Narayanan, Lian Li, Matthew Lek Min Lim, and Daiqin Li

Design of Superior Spider Silk: From Nanostructure to Mechanical Properties
Biophys. J. 2006. 91:4528-4535. [Abstract] [Full Text] [PDF]

Pau Bernado, Martin Blackledge, and Javier Sancho

Sequence-Specific Solvent Accessibilities of Protein Residues in Unfolded Protein Ensembles
Biophys. J. 2006. 91:4536-4543. [Abstract] [Full Text] [PDF]

Voichita M. Dadarlat and Carol Beth Post

Decomposition of Protein Experimental Compressibility into Intrinsic and Hydration Shell Contributions
Biophys. J. 2006. 91:4544-4554. [Abstract] [Full Text] [PDF]

Michael Hayley, Jason Emberley, Philip J. Davis, Michael R. Morrow, and John J. Robinson

Interaction of Toposome from Sea-Urchin Yolk Granules with Dimyristoyl Phosphatidylserine Model Membranes: A ²H-NMR Study
Biophys. J. 2006. 91:4555-4564. [Abstract] [Full Text] [PDF]

Shashi Bhushan Pandit, Yang Zhang, and Jeffrey Skolnick

TASSER-Lite: An Automated Tool for Protein Comparative Modeling
Biophys. J. 2006. 91:4180-4190. [Abstract] [Full Text] [PDF]

Andras D. Kaposi, Jane M. Vanderkooi, and Solomon S. Stavrov

Infrared Absorption Study of the Heme Pocket Dynamics of Carbonmonoxyheme Proteins
Biophys. J. 2006. 91:4191-4200. [Abstract] [Full Text] [PDF]

Minfen Li, Jingxian Liu, Xiaoyuan Ran, Miaoqing Fang, Jiahai Shi, Haina Qin, June-Mui Goh, and Jianxing Song

Resurrecting Abandoned Proteins with Pure Water: CD and NMR Studies of Protein Fragments Solubilized in Salt-Free Water
Biophys. J. 2006. 91:4201-4209. [Abstract] [Full Text] [PDF]

Karin Nienhaus, Fabiana Renzi, Beatrice Vallone, Jorg Wiedenmann, and G. Ulrich Nienhaus

Chromophore-Protein Interactions in the Anthozoan Green Fluorescent Protein asFP499
Biophys. J. 2006. 91:4210-4220. [Abstract] [Full Text] [PDF]

Igor K. Lednev, Vladimir V. Ermolenkov, Seiichiro Higashiya, Ludmila A. Popova, Natalya I. Topilina, and John T. Welch

Reversible Thermal Denaturation of a 60-kDa Genetically Engineered ß-Sheet Polypeptide
Biophys. J. 2006. 91:3805-3818. [Abstract] [Full Text] [PDF]

Ying Li, Aleksandra Z. Kijac, Stephen G. Sligar, and Chad M. Rienstra

Structural Analysis of Nanoscale Self-Assembled Discoidal Lipid Bilayers by Solid-State NMR Spectroscopy
Biophys. J. 2006. 91:3819-3828. [Abstract] [Full Text] [PDF]

Alexis Huet and Philippe Derreumaux

Impact of the Mutation A21G (Flemish Variant) on Alzheimer's ß-Amyloid Dimers by Molecular Dynamics Simulations
Biophys. J. 2006. 91:3829-3840. [Abstract] [Full Text] [PDF]

Yanina A. Goddard, Jean-Pierre Korb, and Robert G. Bryant

Structural and Dynamical Examination of the Low-Temperature Glass Transition in Serum Albumin
Biophys. J. 2006. 91:3841-3847. [Abstract] [Full Text] [PDF]

Eric Miller, Tzintzuni Garcia, Scott Hultgren, and Andres F. Oberhauser

The Mechanical Properties of E. coli Type 1 Pili Measured by Atomic Force Microscopy Techniques
Biophys. J. 2006. 91:3848-3856. [Abstract] [Full Text] [PDF]

S. Stolyarova, E. Saridakis, N. E. Chayen, and Y. Nemirovsky

A Model for Enhanced Nucleation of Protein Crystals on a Fractal Porous Substrate
Biophys. J. 2006. 91:3857-3863. [Abstract] [Full Text] [PDF]

Patrizia Cioni

Role of Protein Cavities on Unfolding Volume Change and on Internal Dynamics under Pressure
Biophys. J. 2006. 91:3390-3396. [Abstract] [Full Text] [PDF]

N. El Kadi, N. Taulier, J. Y. Le Huerou, M. Gindre, W. Urbach, I. Nwigwe, P. C. Kahn, and M. Waks

Unfolding and Refolding of Bovine Serum Albumin at Acid pH: Ultrasound and Structural Studies
Biophys. J. 2006. 91:3397-3404. [Abstract] [Full Text] [PDF]

John H. Streiff, Thomas W. Allen, Elena Atanasova, Nenad Juranic, Slobodan Macura, Alan R. Penheiter, and Keith A. Jones

Prediction of Volatile Anesthetic Binding Sites in Proteins
Biophys. J. 2006. 91:3405-3414. [Abstract] [Full Text] [PDF]

Juan Jaspe and Stephen J. Hagen

Do Protein Molecules Unfold in a Simple Shear Flow?
Biophys. J. 2006. 91:3415-3424. [Abstract] [Full Text] [PDF]

Nitin Rathore, Samuel H. Gellman, and Juan J. de Pablo

Thermodynamic Stability of ß-Peptide Helices and the Role of Cyclic Residues
Biophys. J. 2006. 91:3425-3435. [Abstract] [Full Text] [PDF]

Sterling Paramore and Gregory A. Voth

Examining the Influence of Linkers and Tertiary Structure in the Forced Unfolding of Multiple-Repeat Spectrin Molecules
Biophys. J. 2006. 91:3436-3445. [Abstract] [Full Text] [PDF]

Nathan Duff, N.-H. Duong, and Daniel J. Lacks

Stretching the Immunoglobulin 27 Domain of the Titin Protein: The Dynamic Energy Landscape
Biophys. J. 2006. 91:3446-3455. [Abstract] [Full Text] [PDF]

Semen O. Yesylevskyy, Valery N. Kharkyanen, and Alexander P. Demchenko

The Change of Protein Intradomain Mobility on Ligand Binding: Is It a Commonly Observed Phenomenon?
Biophys. J. 2006. 91:3002-3013. [Abstract] [Full Text] [PDF]

I. Digel, Ch. Maggakis-Kelemen, K. F. Zerlin, Pt. Linder, N. Kasischke, P. Kayser, D. Porst, A. Temiz Artmann, and G. M. Artmann

Body Temperature-Related Structural Transitions of Monotremal and Human Hemoglobin
Biophys. J. 2006. 91:3014-3021. [Abstract] [Full Text] [PDF]

Enrica Droghetti, Silke Oellerich, Peter Hildebrandt, and Giulietta Smulevich

Heme Coordination States of Unfolded Ferrous Cytochrome c
Biophys. J. 2006. 91:3022-3031. [Abstract] [Full Text] [PDF]

Sang Ho Park, Anna A. De Angelis, Alexander A. Nevzorov, Chin H. Wu, and Stanley J. Opella

Three-Dimensional Structure of the Transmembrane Domain of Vpu from HIV-1 in Aligned Phospholipid Bicelles
Biophys. J. 2006. 91:3032-3042. [Abstract] [Full Text] [PDF]

Gabor Papp, Beata Bugyi, Zoltan Ujfalusi, Szilvia Barko, Gabor Hild, Bela Somogyi, and Miklos Nyitrai

Conformational Changes in Actin Filaments Induced by Formin Binding to the Barbed End
Biophys. J. 2006. 91:2564-2572. [Abstract] [Full Text] [PDF]

J. H. Roh, J. E. Curtis, S. Azzam, V. N. Novikov, I. Peral, Z. Chowdhuri, R. B. Gregory, and A. P. Sokolov

Influence of Hydration on the Dynamics of Lysozyme
Biophys. J. 2006. 91:2573-2588. [Abstract] [Full Text] [PDF]

Esmael J. Haddadian and Elizabeth L. Gross

A Brownian Dynamics Study of the Interactions of the Luminal Domains of the Cytochrome b₆f complex with Plastocyanin and Cytochrome c₆: The Effects of the Rieske FeS Protein on the Interactions
Biophys. J. 2006. 91:2589-2600. [Abstract] [Full Text] [PDF]

Laura Treccani, Karlheinz Mann, Fabian Heinemann, and Monika Fritz

Perlwapin, an Abalone Nacre Protein with Three Four-Disulfide Core (Whey Acidic Protein) Domains, Inhibits the Growth of Calcium Carbonate Crystals
Biophys. J. 2006. 91:2601-2608. [Abstract] [Full Text] [PDF]

Leslie M. Hicks, Carl J. Balibar, Christopher T. Walsh, Neil L. Kelleher, and Nathan J. Hillson

Probing Intra- versus Interchain Kinetic Preferences of L-Thr Acylation on Dimeric VibF with Mass Spectrometry
Biophys. J. 2006. 91:2609-2619. [Abstract] [Full Text] [PDF]

P. Tompa, P. Banki, M. Bokor, P. Kamasa, D. Kovacs, G. Lasanda, and K. Tompa

Protein-Water and Protein-Buffer Interactions in the Aqueous Solution of an Intrinsically Unstructured Plant Dehydrin: NMR Intensity and DSC Aspects
Biophys. J. 2006. 91:2243-2249. [Abstract] [Full Text] [PDF]

Ines Garcia-Rubio, Milagros Medina, Richard Cammack, Pablo J. Alonso, and Jesus I. Martinez

CW-EPR and ENDOR Study of Cytochrome c₆ from Anabaena PCC 7119
Biophys. J. 2006. 91:2250-2263. [Abstract] [Full Text] [PDF]

J. Font, J. Torrent, M. Ribo, D. V. Laurents, C. Balny, M. Vilanova, and R. Lange

Pressure-Jump-Induced Kinetics Reveals a Hydration Dependent Folding/Unfolding Mechanism of Ribonuclease A
Biophys. J. 2006. 91:2264-2274. [Abstract] [Full Text] [PDF]

Steven Hayward and Akio Kitao

Molecular Dynamics Simulations of NAD⁺-Induced Domain Closure in Horse Liver Alcohol Dehydrogenase
Biophys. J. 2006. 91:1823-1831. [Abstract] [Full Text] [PDF]

Vaithiyalingam Sivaraja, Thallapuranam Krishnaswamy Suresh Kumar, Dakshinamurthy Rajalingam, Irene Graziani, Igor Prudovsky, and Chin Yu

Copper Binding Affinity of S100A13, a Key Component of the FGF-1 Nonclassical Copper-Dependent Release Complex
Biophys. J. 2006. 91:1832-1843. [Abstract] [Full Text] [PDF]

Jordi Cohen, Anton Arkhipov, Rosemary Braun, and Klaus Schulten

Imaging the Migration Pathways for O₂, CO, NO, and Xe Inside Myoglobin
Biophys. J. 2006. 91:1844-1857. [Abstract] [Full Text] [PDF]

Ying Xiong, Hai-Ting Lu, Yongjian Li, Guang-Fu Yang, and Chang-Guo Zhan

Characterization of a Catalytic Ligand Bridging Metal Ions in Phosphodiesterases 4 and 5 by Molecular Dynamics Simulations and Hybrid Quantum Mechanical/Molecular Mechanical Calculations
Biophys. J. 2006. 91:1858-1867. [Abstract] [Full Text] [PDF]

Hoang T. Tran and Rohit V. Pappu

Toward an Accurate Theoretical Framework for Describing Ensembles for Proteins under Strongly Denaturing Conditions
Biophys. J. 2006. 91:1868-1886. [Abstract] [Full Text] [PDF]

Adrian Velazquez-Campoy, Guillermina Goni, Jose Ramon Peregrina, and Milagros Medina

Exact Analysis of Heterotropic Interactions in Proteins: Characterization of Cooperative Ligand Binding by Isothermal Titration Calorimetry
Biophys. J. 2006. 91:1887-1904. [Abstract] [Full Text] [PDF]

Colette A. Sacksteder, Jennifer E. Whittier, Yijia Xiong, Jinhui Li, Nadezhda A. Galeva, Michael E. Jacoby, Samuel O. Purvine, Todd D. Williams, Martin C. Rechsteiner, Diana J. Bigelow, and Thomas C. Squier

Tertiary Structural Rearrangements upon Oxidation of Methionine¹⁴⁵ in Calmodulin Promotes Targeted Proteasomal Degradation
Biophys. J. 2006. 91:1480-1493. [Abstract] [Full Text] [PDF]

Tuomas P. J. Knowles and Ralph Zahn

Enhanced Stability of Human Prion Proteins with Two Disulfide Bridges
Biophys. J. 2006. 91:1494-1500. [Abstract] [Full Text] [PDF]

Jaume Torres, Krupakar Parthasarathy, Xin Lin, Rathi Saravanan, Andreas Kukol, and Ding Xiang Liu

Model of a Putative Pore: The Pentameric -Helical Bundle of SARS Coronavirus E Protein in Lipid Bilayers
Biophys. J. 2006. 91:938-947. [Abstract] [Full Text] [PDF]

Xin Hu and C. Erec Stebbins

Dynamics of the WPD Loop of the Yersinia Protein Tyrosine Phosphatase
Biophys. J. 2006. 91:948-956. [Abstract] [Full Text] [PDF]

Yraima Cordeiro, Julia Kraineva, Marisa Carvalho Suarez, Anna Gabriella Tempesta, Jeffery W. Kelly, Jerson L. Silva, Roland Winter, and Debora Foguel

Fourier Transform Infrared Spectroscopy Provides a Fingerprint for the Tetramer and for the Aggregates of Transthyretin
Biophys. J. 2006. 91:957-967. [Abstract] [Full Text] [PDF]

Sergio Giuffrida, Grazia Cottone, and Lorenzo Cordone

Role of Solvent on Protein-Matrix Coupling in MbCO Embedded in Water-Saccharide Systems: A Fourier Transform Infrared Spectroscopy Study
Biophys. J. 2006. 91:968-980. [Abstract] [Full Text] [PDF]

Bjorn U. Klink, Roger S. Goody, and Axel J. Scheidig

A Newly Designed Microspectrofluorometer for Kinetic Studies on Protein Crystals in Combination with X-Ray Diffraction
Biophys. J. 2006. 91:981-992. [Abstract] [Full Text] [PDF]

Ian M. Hodge

Application of the Thermorheologically Complex Nonlinear Adam-Gibbs Model for the Glass Transition to Molecular Motion in Hydrated Proteins
Biophys. J. 2006. 91:993-995. [Abstract] [Full Text] [PDF]

John Simms, Debbie L. Hay, Mark Wheatley, and David R. Poyner

Characterization of the Structure of RAMP1 by Mutagenesis and Molecular Modeling
Biophys. J. 2006. 91:662-669. [Abstract] [Full Text] [PDF]

Semen O. Yesylevskyy, Valery N. Kharkyanen, and Alexander P. Demchenko

Dynamic Protein Domains: Identification, Interdependence, and Stability
Biophys. J. 2006. 91:670-685. [Abstract] [Full Text] [PDF]

Sung-Hye Kim, Jun Zhang, Yan Jiang, Hai-Meng Zhou, and Yong-Bin Yan

Assisting the Reactivation of Guanidine Hydrochloride-Denatured Aminoacylase by Hydroxypropyl Cyclodextrins
Biophys. J. 2006. 91:686-693. [Abstract] [Full Text] [PDF]

Fabio Cecconi, Carlo Guardiani, and Roberto Livi

Testing Simplified Proteins Models of the hPin1 WW Domain
Biophys. J. 2006. 91:694-704. [Abstract] [Full Text] [PDF]

Danny G. Hill and John E. Baenziger

The Net Orientation of Nicotinic Receptor Transmembrane -Helices in the Resting and Desensitized States
Biophys. J. 2006. 91:705-714. [Abstract] [Full Text] [PDF]

Christian D. Geierhaas, Robert B. Best, Emanuele Paci, Michele Vendruscolo, and Jane Clarke

Structural Comparison of the Two Alternative Transition States for Folding of TI I27
Biophys. J. 2006. 91:263-275. [Abstract] [Full Text] [PDF]

Marco Buscaglia, Lisa J. Lapidus, William A. Eaton, and James Hofrichter

Effects of Denaturants on the Dynamics of Loop Formation in Polypeptides
Biophys. J. 2006. 91:276-288. [Abstract] [Full Text] [PDF]

E. Cornicchi, M. Marconi, G. Onori, and A. Paciaroni

Controlling the Protein Dynamical Transition with Sugar-Based Bioprotectant Matrices: A Neutron Scattering Study
Biophys. J. 2006. 91:289-297. [Abstract] [Full Text] [PDF]

Katherine L. Gudiksen, Irina Gitlin, Demetri T. Moustakas, and George M. Whitesides

Increasing the Net Charge and Decreasing the Hydrophobicity of Bovine Carbonic Anhydrase Decreases the Rate of Denaturation with Sodium Dodecyl Sulfate
Biophys. J. 2006. 91:298-310. [Abstract] [Full Text] [PDF]

Kelly L. Damm and Heather A. Carlson

Gaussian-Weighted RMSD Superposition of Proteins: A Structural Comparison for Flexible Proteins and Predicted Protein Structures
Biophys. J. 2006. 90:4558-4573. [Abstract] [Full Text] [PDF]

Alexander J. Marchut and Carol K. Hall

Side-Chain Interactions Determine Amyloid Formation by Model Polyglutamine Peptides in Molecular Dynamics Simulations
Biophys. J. 2006. 90:4574-4584. [Abstract] [Full Text] [PDF]

Mauro Manno, Emanuela Fabiola Craparo, Vincenzo Martorana, Donatella Bulone, and Pier Luigi San Biagio

Kinetics of Insulin Aggregation: Disentanglement of Amyloid Fibrillation from Large-Size Cluster Formation
Biophys. J. 2006. 90:4585-4591. [Abstract] [Full Text] [PDF]

Estefania Hurtado-Gomez, Gregorio Fernandez-Ballester, Harald Nothaft, Javier Gomez, Fritz Titgemeyer, and Jose Luis Neira

Biophysical Characterization of the Enzyme I of the Streptomyces coelicolor Phosphoenolpyruvate:Sugar Phosphotransferase System
Biophys. J. 2006. 90:4592-4604. [Abstract] [Full Text] [PDF]

Oana Coban, Don C. Lamb, Evgeny Zaychikov, Hermann Heumann, and G. Ulrich Nienhaus

Conformational Heterogeneity in RNA Polymerase Observed by Single-Pair FRET Microscopy
Biophys. J. 2006. 90:4605-4617. [Abstract] [Full Text] [PDF]

Arwel V. Hughes, Paul Rees, Peter Heathcote, and Michael R. Jones

Kinetic Analysis of the Thermal Stability of the Photosynthetic Reaction Center from Rhodobacter sphaeroides
Biophys. J. 2006. 90:4155-4166. [Abstract] [Full Text] [PDF]

Manish C. Saraf, Gregory L. Moore, Nina M. Goodey, Vania Y. Cao, Stephen J. Benkovic, and Costas D. Maranas

IPRO: An Iterative Computational Protein Library Redesign and Optimization Procedure
Biophys. J. 2006. 90:4167-4180. [Abstract] [Full Text] [PDF]

Jesper Sondergaard Pedersen, James M. Flink, Dantcho Dikov, and Daniel Erik Otzen

Sulfates Dramatically Stabilize a Salt-Dependent Type of Glucagon Fibrils
Biophys. J. 2006. 90:4181-4194. [Abstract] [Full Text] [PDF]

Mohammad Delawar Hossain, Shou Furuike, Yasushi Maki, Kengo Adachi, M. Yusuf Ali, Mominul Huq, Hiroyasu Itoh, Masasuke Yoshida, and Kazuhiko Kinosita Jr.

The Rotor Tip Inside a Bearing of a Thermophilic F₁-ATPase Is Dispensable for Torque Generation
Biophys. J. 2006. 90:4195-4203. [Abstract] [Full Text] [PDF]

Simone Melchionna, Raffaele Sinibaldi, and Giuseppe Briganti

Explanation of the Stability of Thermophilic Proteins Based on Unique Micromorphology
Biophys. J. 2006. 90:4204-4212. [Abstract] [Full Text] [PDF]

David L. Stokes, Andrew J. Pomfret, William J. Rice, John Paul Glaves, and Howard S. Young

Interactions between Ca²⁺-ATPase and the Pentameric Form of Phospholamban in Two-Dimensional Co-Crystals
Biophys. J. 2006. 90:4213-4223. [Abstract] [Full Text] [PDF]

Simon F. Tolic-Norrelykke, Mette B. Rasmussen, Francesco S. Pavone, Kirstine Berg-Sorensen, and Lene B. Oddershede

Stepwise Bending of DNA by a Single TATA-Box Binding Protein
Biophys. J. 2006. 90:3694-3703. [Abstract] [Full Text] [PDF]

C. Duy and J. Fitter

How Aggregation and Conformational Scrambling of Unfolded States Govern Fluorescence Emission Spectra
Biophys. J. 2006. 90:3704-3711. [Abstract] [Full Text] [PDF]

Eliana D. Grimm, Rodrigo V. Portugal, Mario de Oliveira Neto, Nadia H. Martins, Igor Polikarpov, Arnaldo Zaha, and Henrique B. Ferreira

Structural Analysis of an Echinococcus granulosus Actin-Fragmenting Protein by Small-Angle X-Ray Scattering Studies and Molecular Modeling
Biophys. J. 2006. 90:3216-3223. [Abstract] [Full Text] [PDF]

Diannan Lu, Zheng Liu, and Jianzhong Wu

Structural Transitions of Confined Model Proteins: Molecular Dynamics Simulation and Experimental Validation
Biophys. J. 2006. 90:3224-3238. [Abstract] [Full Text] [PDF]

Edi Gabellieri and Giovanni B. Strambini

ANS Fluorescence Detects Widespread Perturbations of Protein Tertiary Structure in Ice
Biophys. J. 2006. 90:3239-3245. [Abstract] [Full Text] [PDF]

Jonathan P. Williams, Daniel C. Smith, Brian N. Green, Brian D. Marsden, Keith R. Jennings, Lynne M. Roberts, and James H. Scrivens

Gas Phase Characterization of the Noncovalent Quaternary Structure of Cholera Toxin and the Cholera Toxin B Subunit Pentamer
Biophys. J. 2006. 90:3246-3254. [Abstract] [Full Text] [PDF]

Inna Y. Churbanova, Andrey Tronin, Joseph Strzalka, Thomas Gog, Ivan Kuzmenko, Jonas S. Johansson, and J. Kent Blasie

Monolayers of a Model Anesthetic-Binding Membrane Protein: Formation, Characterization, and Halothane-Binding Affinity
Biophys. J. 2006. 90:3255-3266. [Abstract] [Full Text] [PDF]

Mu Gao and Klaus Schulten

Onset of Anthrax Toxin Pore Formation
Biophys. J. 2006. 90:3267-3279. [Abstract] [Full Text] [PDF]

Jennifer M. Bui, Zoran Radic, Palmer Taylor, and J. Andrew McCammon

Conformational Transitions in Protein-Protein Association: Binding of Fasciculin-2 to Acetylcholinesterase
Biophys. J. 2006. 90:3280-3287. [Abstract] [Full Text] [PDF]

Ingemar Andre, Tonu Kesvatera, Bo Jonsson, and Sara Linse

Salt Enhances Calmodulin-Target Interaction
Biophys. J. 2006. 90:2903-2910. [Abstract] [Full Text] [PDF]

Stina Lindman, Wei-Feng Xue, Olga Szczepankiewicz, Mikael C. Bauer, Hanna Nilsson, and Sara Linse

Salting the Charged Surface: pH and Salt Dependence of Protein G B1 Stability
Biophys. J. 2006. 90:2911-2921. [Abstract] [Full Text] [PDF]

Miyeon Kim, Qi Xu, Gail E. Fanucci, and David S. Cafiso

Solutes Modify a Conformational Transition in a Membrane Transport Protein
Biophys. J. 2006. 90:2922-2929. [Abstract] [Full Text] [PDF]

Wei Yuan Yang and Martin Gruebele

Binary and Ternary Aggregation within Tethered Protein Constructs
Biophys. J. 2006. 90:2930-2937. [Abstract] [Full Text] [PDF]

Ashutosh Kumar, Sudha Srivastava, Ram Kumar Mishra, Rohit Mittal, and Ramakrishna V. Hosur

Local Structural Preferences and Dynamics Restrictions in the Urea-Denatured State of SUMO-1: NMR Characterization
Biophys. J. 2006. 90:2498-2509. [Abstract] [Full Text] [PDF]

Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Leif A. Eriksson, and Maria Joao Ramos

Dehydration of Ribonucleotides Catalyzed by Ribonucleotide Reductase: The Role of the Enzyme
Biophys. J. 2006. 90:2109-2119. [Abstract] [Full Text] [PDF]

Sarah Batey, Kathryn A. Scott, and Jane Clarke

Complex Folding Kinetics of a Multidomain Protein
Biophys. J. 2006. 90:2120-2130. [Abstract] [Full Text] [PDF]

Ole Farver, Ernst Grell, Bernd Ludwig, Hartmut Michel, and Israel Pecht

Rates and Equilibrium of Cu_A to Heme a Electron Transfer in Paracoccus denitrificans Cytochrome c Oxidase
Biophys. J. 2006. 90:2131-2137. [Abstract] [Full Text] [PDF]

Kausiki Datta, Andy J. Wowor, Allison J. Richard, and Vince J. LiCata

Temperature Dependence and Thermodynamics of Klenow Polymerase Binding to Primed-Template DNA
Biophys. J. 2006. 90:1739-1751. [Abstract] [Full Text] [PDF]

Jochen Zimmer, Declan A. Doyle, and J. Gunter Grossmann

Structural Characterization and pH-Induced Conformational Transition of Full-Length KcsA
Biophys. J. 2006. 90:1752-1766. [Abstract] [Full Text] [PDF]

Nitin Rathore, Thomas A. Knotts IV, and Juan J. de Pablo

Confinement Effects on the Thermodynamics of Protein Folding: Monte Carlo Simulations
Biophys. J. 2006. 90:1767-1773. [Abstract] [Full Text] [PDF]

Francesca Bernardi, Elena Gaggelli, Elena Molteni, Elena Porciatti, Daniela Valensin, and Gianni Valensin

¹H and ¹³C-NMR and Molecular Dynamics Studies of Cyclosporin A Interacting with Magnesium(II) or Cerium(III) in Acetonitrile. Conformational Changes and cis-trans Conversion of Peptide Bonds
Biophys. J. 2006. 90:1350-1361. [Abstract] [Full Text] [PDF]

Eitan Gross, Dao-Quan Peng, Stanley L. Hazen, and Jonathan D. Smith

A Novel Folding Intermediate State for Apolipoprotein A-I: Role of the Amino and Carboxy Termini
Biophys. J. 2006. 90:1362-1370. [Abstract] [Full Text] [PDF]

Sebastien Courty, Joanne L. Gornall, and Eugene M. Terentjev

Mechanically Induced Helix-Coil Transition in Biopolymer Networks
Biophys. J. 2006. 90:1019-1027. [Abstract] [Full Text] [PDF]

Katsuya Shimabukuro, Eiro Muneyuki, and Masasuke Yoshida

An Alternative Reaction Pathway of F₁-ATPase Suggested by Rotation without 80°/40° Substeps of a Sluggish Mutant at Low ATP
Biophys. J. 2006. 90:1028-1032. [Abstract] [Full Text] [PDF]

Robert F. Pasternack, Esther J. Gibbs, Scott Sibley, Lauren Woodard, Peter Hutchinson, Joseph Genereux, and Kathleen Kristian

Formation Kinetics of Insulin-Based Amyloid Gels and the Effect of Added Metalloporphyrins
Biophys. J. 2006. 90:1033-1042. [Abstract] [Full Text] [PDF]

Esmael J. Haddadian and Elizabeth L. Gross

A Brownian Dynamics Study of the Effects of Cytochrome f Structure and Deletion of Its Small Domain in Interactions with Cytochrome c₆ and Plastocyanin in Chlamydomonas reinhardtii
Biophys. J. 2006. 90:566-577. [Abstract] [Full Text] [PDF]

Randall J. Radmer and Teri E. Klein

Triple Helical Structure and Stabilization of Collagen-like Molecules with 4(R)-Hydroxyproline in the Xaa Position
Biophys. J. 2006. 90:578-588. [Abstract] [Full Text] [PDF]

Alessandro Podesta, Guido Tiana, Paolo Milani, and Mauro Manno

Early Events in Insulin Fibrillization Studied by Time-Lapse Atomic Force Microscopy
Biophys. J. 2006. 90:589-597. [Abstract] [Full Text] [PDF]

Mei M. Whittaker, Kazunori Mizuno, Hans Peter Bachinger, and James W. Whittaker

Kinetic Analysis of the Metal Binding Mechanism of Escherichia coli Manganese Superoxide Dismutase
Biophys. J. 2006. 90:598-607. [Abstract] [Full Text] [PDF]

Meng Qin, Jian Zhang, and Wei Wang

Effects of Disulfide Bonds on Folding Behavior and Mechanism of the ß-Sheet Protein Tendamistat
Biophys. J. 2006. 90:272-286. [Abstract] [Full Text] [PDF]

Daniel K. West, David J. Brockwell, Peter D. Olmsted, Sheena E. Radford, and Emanuele Paci

Mechanical Resistance of Proteins Explained Using Simple Molecular Models
Biophys. J. 2006. 90:287-297. [Abstract] [Full Text] [PDF]

Charles Chow, Nese Kurt, Regina M. Murphy, and Silvia Cavagnero

Structural Characterization of Apomyoglobin Self-Associated Species in Aqueous Buffer and Urea Solution
Biophys. J. 2006. 90:298-309. [Abstract] [Full Text] [PDF]

Vladimir A. Goncharov

Mass Spectroscopic Analysis of Sup35NM Prion Polymerization
Biophys. J. 2005. 89:4139-4148. [Abstract] [Full Text] [PDF]

Zhicheng Xia, Bao D. Nguyen, Maurizio Brunori, Francesca Cutruzzola, and Gerd N. La Mar

¹H-NMR Study of the Effect of Temperature through Reversible Unfolding on the Heme Pocket Molecular Structure and Magnetic Properties of Aplysia limacina Cyano-Metmyoglobin
Biophys. J. 2005. 89:4149-4158. [Abstract] [Full Text] [PDF]

K. V. Brinda and Saraswathi Vishveshwara

A Network Representation of Protein Structures: Implications for Protein Stability
Biophys. J. 2005. 89:4159-4170. [Abstract] [Full Text] [PDF]

Idelisa Ayala, J. Jefferson P. Perry, Jan Szczepanski, John A. Tainer, Martin T. Vala, Harry S. Nick, and David N. Silverman

Hydrogen Bonding in Human Manganese Superoxide Dismutase Containing 3-Fluorotyrosine
Biophys. J. 2005. 89:4171-4179. [Abstract] [Full Text] [PDF]

Ting Wang, Wai Leung Lau, William F. DeGrado, and Feng Gai

T-Jump Infrared Study of the Folding Mechanism of Coiled-Coil GCN4-p1
Biophys. J. 2005. 89:4180-4187. [Abstract] [Full Text] [PDF]

Jose A. Hernandez, Jorg Meier, Francisco N. Barrera, Olga Ruiz de los Panos, Estefania Hurtado-Gomez, M. Teresa Bes, Maria F. Fillat, M. Luisa Peleato, Claudio N. Cavasotto, and Jose L. Neira

The Conformational Stability and Thermodynamics of Fur A (Ferric Uptake Regulator) from Anabaena sp. PCC 7119
Biophys. J. 2005. 89:4188-4200. [Abstract] [Full Text] [PDF]

Martino Calamai, Fabrizio Chiti, and Christopher M. Dobson

Amyloid Fibril Formation Can Proceed from Different Conformations of a Partially Unfolded Protein
Biophys. J. 2005. 89:4201-4210. [Abstract] [Full Text] [PDF]

Joseph J. Valente, Kusum S. Verma, Mark Cornell Manning, W. William Wilson, and Charles S. Henry

Second Virial Coefficient Studies of Cosolvent-Induced Protein Self-Interaction
Biophys. J. 2005. 89:4211-4218. [Abstract] [Full Text] [PDF]

Mario Pujato, Clay Bracken, Romina Mancusso, Marcela Cataldi, and Maria Luisa Tasayco

pH Dependence of Amide Chemical Shifts in Natively Disordered Polypeptides Detects Medium-Range Interactions with Ionizable Residues
Biophys. J. 2005. 89:3293-3302. [Abstract] [Full Text] [PDF]

F. Gabel, M. Weik, P. Masson, F. Renault, D. Fournier, L. Brochier, B. P. Doctor, A. Saxena, I. Silman, and G. Zaccai

Effects of Soman Inhibition and of Structural Differences on Cholinesterase Molecular Dynamics: A Neutron Scattering Study
Biophys. J. 2005. 89:3303-3311. [Abstract] [Full Text] [PDF]

Xavier Siebert, Betty A. Eipper, Richard E. Mains, Sean T. Prigge, Ninian J. Blackburn, and L. Mario Amzel

The Catalytic Copper of Peptidylglycine -Hydroxylating Monooxygenase also Plays a Critical Structural Role
Biophys. J. 2005. 89:3312-3319. [Abstract] [Full Text] [PDF]

Raquel Godoy-Ruiz, Raul Perez-Jimenez, Beatriz Ibarra-Molero, and Jose M. Sanchez-Ruiz

A Stability Pattern of Protein Hydrophobic Mutations that Reflects Evolutionary Structural Optimization
Biophys. J. 2005. 89:3320-3331. [Abstract] [Full Text] [PDF]

Kathryn Luke, David Apiyo, and Pernilla Wittung-Stafshede

Dissecting Homo-Heptamer Thermodynamics by Isothermal Titration Calorimetry: Entropy-Driven Assembly of Co-Chaperonin Protein 10
Biophys. J. 2005. 89:3332-3336. [Abstract] [Full Text] [PDF]

Sri Rama Koti Ainavarapu, Lewyn Li, Carmen L. Badilla, and Julio M. Fernandez

Ligand Binding Modulates the Mechanical Stability of Dihydrofolate Reductase
Biophys. J. 2005. 89:3337-3344. [Abstract] [Full Text] [PDF]

Dhasakumar Navaratnam, Jun-Ping Bai, Haresha Samaranayake, and Joseph Santos-Sacchi

N-Terminal-Mediated Homomultimerization of Prestin, the Outer Hair Cell Motor Protein
Biophys. J. 2005. 89:3345-3352. [Abstract] [Full Text] [PDF]

Maksim Kouza, Chi-Fon Chang, Shura Hayryan, Tsan-hung Yu, Mai Suan Li, Tai-huang Huang, and Chin-Kun Hu

Folding of the Protein Domain hbSBD
Biophys. J. 2005. 89:3353-3361. [Abstract] [Full Text] [PDF]

Thomas Stockner, Hans J. Vogel, and D. Peter Tieleman

A Salt-Bridge Motif Involved in Ligand Binding and Large-Scale Domain Motions of the Maltose-Binding Protein
Biophys. J. 2005. 89:3362-3371. [Abstract] [Full Text] [PDF]

Christina S. Strom, Xiang Yang Liu, and Zongchao Jia

Why Does Insect Antifreeze Protein from Tenebrio molitor Produce Pyramidal Ice Crystallites?
Biophys. J. 2005. 89:2618-2627. [Abstract] [Full Text] [PDF]

A. Iulia Ioanitescu, Sylvia Dewilde, Laurent Kiger, Michael C. Marden, Luc Moens, and Sabine Van Doorslaer

Characterization of Nonsymbiotic Tomato Hemoglobin
Biophys. J. 2005. 89:2628-2639. [Abstract] [Full Text] [PDF]

V. M. Bolanos-Garcia, S. Beaufils, A. Renault, J. G. Grossmann, S. Brewerton, M. Lee, A. Venkitaraman, and T. L. Blundell

The Conserved N-Terminal Region of the Mitotic Checkpoint Protein BUBR1: A Putative TPR Motif of High Surface Activity
Biophys. J. 2005. 89:2640-2649. [Abstract] [Full Text] [PDF]

Hua-Wei He, Jun Zhang, Hai-Meng Zhou, and Yong-Bin Yan

Conformational Change in the C-Terminal Domain Is Responsible for the Initiation of Creatine Kinase Thermal Aggregation
Biophys. J. 2005. 89:2650-2658. [Abstract] [Full Text] [PDF]

Scott M. Stagg and Stephen C. Harvey

Exploring the Flexibility of Ribosome Recycling Factor Using Molecular Dynamics
Biophys. J. 2005. 89:2659-2666. [Abstract] [Full Text] [PDF]

Yraima Cordeiro, Julia Kraineva, Mariana P. B. Gomes, Marilene H. Lopes, Vilma R. Martins, Luis M. T. R. Lima, Debora Foguel, Roland Winter, and Jerson L. Silva

The Amino-Terminal PrP Domain Is Crucial to Modulate Prion Misfolding and Aggregation
Biophys. J. 2005. 89:2667-2676. [Abstract] [Full Text] [PDF]

Maria A. Rotter, Suzanna Kwong, Robin W. Briehl, and Frank A. Ferrone

Heterogeneous Nucleation in Sickle Hemoglobin: Experimental Validation of a Structural Mechanism
Biophys. J. 2005. 89:2677-2684. [Abstract] [Full Text] [PDF]

Jean-Pierre Korb and Robert G. Bryant

Noise and Functional Protein Dynamics
Biophys. J. 2005. 89:2685-2692. [Abstract] [Full Text] [PDF]

Jorge Chahine and Margaret S. Cheung

Computational Studies of the Reversible Domain Swapping of p13suc1
Biophys. J. 2005. 89:2693-2700. [Abstract] [Full Text] [PDF]

Yuichi Harano and Masahiro Kinoshita

Translational-Entropy Gain of Solvent upon Protein Folding
Biophys. J. 2005. 89:2701-2710. [Abstract] [Full Text] [PDF]

Judit Osz, Gabriella Bodo, Rui Miguel Mamede Branca, and Csaba Bagyinka

Theoretical Calculations on Hydrogenase Kinetics: Explanation of the Lag Phase and the Enzyme Concentration Dependence of the Activity of Hydrogenase Uptake
Biophys. J. 2005. 89:1957-1964. [Abstract] [Full Text] [PDF]

Katherine Abold Todorov, Xiao-Jian Tan, Susanne T. Nonekowski, George A. Garcia, and Heather A. Carlson

The Role of Aspartic Acid 143 in E. coli tRNA-Guanine Transglycosylase: Insights from Mutagenesis Studies and Computational Modeling
Biophys. J. 2005. 89:1965-1977. [Abstract] [Full Text] [PDF]

Marc Niebuhr and Michel H. J. Koch

Effects of Urea and Trimethylamine-N-Oxide (TMAO) on the Interactions of Lysozyme in Solution
Biophys. J. 2005. 89:1978-1983. [Abstract] [Full Text] [PDF]

Judit Osz and Csaba Bagyinka

An Autocatalytic Step in the Reaction Cycle of Hydrogenase from Thiocapsa roseopersicina Can Explain the Special Characteristics of the Enzyme Reaction
Biophys. J. 2005. 89:1984-1989. [Abstract] [Full Text] [PDF]

Angela S. F. Ramos and Simone Techert

Influence of the Water Structure on the Acetylcholinesterase Efficiency
Biophys. J. 2005. 89:1990-2003. [Abstract] [Full Text] [PDF]

Shinpei Nishida, Tomokazu Nada, and Masahide Terazima

Hydrogen Bonding Dynamics during Protein Folding of Reduced Cytochrome c: Temperature and Denaturant Concentration Dependence
Biophys. J. 2005. 89:2004-2010. [Abstract] [Full Text] [PDF]

Leandro Martinez, Milton T. Sonoda, Paul Webb, John D. Baxter, Munir S. Skaf, and Igor Polikarpov

Molecular Dynamics Simulations Reveal Multiple Pathways of Ligand Dissociation from Thyroid Hormone Receptors
Biophys. J. 2005. 89:2011-2023. [Abstract] [Full Text] [PDF]

Sebastian McClendon, Nick Zhadin, and Robert Callender

The Approach to the Michaelis Complex in Lactate Dehydrogenase: The Substrate Binding Pathway
Biophys. J. 2005. 89:2024-2032. [Abstract] [Full Text] [PDF]

Fabio Cannone, Sara Bologna, Barbara Campanini, Alberto Diaspro, Stefano Bettati, Andrea Mozzarelli, and Giuseppe Chirico

Tracking Unfolding and Refolding of Single GFPmut2 Molecules
Biophys. J. 2005. 89:2033-2045. [Abstract] [Full Text] [PDF]

Wenzhe Ma, Chao Tang, and Luhua Lai

Specificity of Trypsin and Chymotrypsin: Loop-Motion-Controlled Dynamic Correlation as a Determinant
Biophys. J. 2005. 89:1183-1193. [Abstract] [Full Text] [PDF]

Wei Liu, Evan Crocker, Stefan N. Constantinescu, and Steven O. Smith

Helix Packing and Orientation in the Transmembrane Dimer of gp55-P of the Spleen Focus Forming Virus
Biophys. J. 2005. 89:1194-1202. [Abstract] [Full Text] [PDF]

Shigenori Nagatomo, Masako Nagai, Yasuhisa Mizutani, Takashi Yonetani, and Teizo Kitagawa

Quaternary Structures of Intermediately Ligated Human Hemoglobin A and Influences from Strong Allosteric Effectors: Resonance Raman Investigation
Biophys. J. 2005. 89:1203-1213. [Abstract] [Full Text] [PDF]

Goran Larsson, Jurgen Schleucher, Jacqueline Onions, Stefan Hermann, Thomas Grundstrom, and Sybren S. Wijmenga

Backbone Dynamics of a Symmetric Calmodulin Dimer in Complex with the Calmodulin-Binding Domain of the Basic-Helix-Loop-Helix Transcription Factor SEF2-1/E2-2: A Highly Dynamic Complex
Biophys. J. 2005. 89:1214-1226. [Abstract] [Full Text] [PDF]

Roger Parker, Timothy R. Noel, Geoffrey J. Brownsey, Katrin Laos, and Stephen G. Ring

The Nonequilibrium Phase and Glass Transition Behavior of ß-Lactoglobulin
Biophys. J. 2005. 89:1227-1236. [Abstract] [Full Text] [PDF]

Dmitri R. Davydov, Alexandra E. Botchkareva, Nadezhda E. Davydova, and James R. Halpert

Resolution of Two Substrate-Binding Sites in an Engineered Cytochrome P450eryF Bearing a Fluorescent Probe
Biophys. J. 2005. 89:418-432. [Abstract] [Full Text] [PDF]

Mingfeng Yang, Ming Lei, Rafael Bruschweiler, and Shuanghong Huo

Initial Conformational Changes of Human Transthyretin under Partially Denaturing Conditions
Biophys. J. 2005. 89:433-443. [Abstract] [Full Text] [PDF]

Laurie S. Sanii, Alex W. Schill, Cristin E. Moran, and Mostafa A. El-Sayed

The Protonation-Deprotonation Kinetics of the Protonated Schiff Base in Bicelle Bacteriorhodopsin Crystals
Biophys. J. 2005. 89:444-451. [Abstract] [Full Text] [PDF]

Bryan W. Berger, Roxana Y. Garcia, Abraham M. Lenhoff, Eric W. Kaler, and Clifford R. Robinson

Relating Surfactant Properties to Activity and Solubilization of the Human Adenosine A₃ Receptor
Biophys. J. 2005. 89:452-464. [Abstract] [Full Text] [PDF]

Cecilia Bossa, Andrea Amadei, Isabella Daidone, Massimiliano Anselmi, Beatrice Vallone, Maurizio Brunori, and Alfredo Di Nola

Molecular Dynamics Simulation of Sperm Whale Myoglobin: Effects of Mutations and Trapped CO on the Structure and Dynamics of Cavities
Biophys. J. 2005. 89:465-474. [Abstract] [Full Text] [PDF]

Rommie E. Amaro, Rebecca S. Myers, V. Jo Davisson, and Zaida A. Luthey-Schulten

Structural Elements in IGP Synthase Exclude Water to Optimize Ammonia Transfer
Biophys. J. 2005. 89:475-487. [Abstract] [Full Text] [PDF]

John M. Finke and Jose N. Onuchic

Equilibrium and Kinetic Folding Pathways of a TIM Barrel with a Funneled Energy Landscape
Biophys. J. 2005. 89:488-505. [Abstract] [Full Text] [PDF]

David J. Brockwell, Godfrey S. Beddard, Emanuele Paci, Dan K. West, Peter D. Olmsted, D. Alastair Smith, and Sheena E. Radford

Mechanically Unfolding the Small, Topologically Simple Protein L
Biophys. J. 2005. 89:506-519. [Abstract] [Full Text] [PDF]

Huseyin Kaya, Zhirong Liu, and Hue Sun Chan

Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple G-like Modeling
Biophys. J. 2005. 89:520-535. [Abstract] [Full Text] [PDF]

Laura Rivas, Claudio M. Soares, Antonio M. Baptista, Jalila Simaan, Roberto E. Di Paolo, Daniel H. Murgida, and Peter Hildebrandt

Electric-Field-Induced Redox Potential Shifts of Tetraheme Cytochromes c₃ Immobilized on Self-Assembled Monolayers: Surface-Enhanced Resonance Raman Spectroscopy and Simulation Studies
Biophys. J. 2005. 88:4188-4199. [Abstract] [Full Text] [PDF]

Mikael Lindgren, Karin Sorgjerd, and Per Hammarstrom

Detection and Characterization of Aggregates, Prefibrillar Amyloidogenic Oligomers, and Protofibrils Using Fluorescence Spectroscopy
Biophys. J. 2005. 88:4200-4212. [Abstract] [Full Text] [PDF]

Patrizia Cioni, Emilia Bramanti, and Giovanni B. Strambini

Effects of Sucrose on the Internal Dynamics of Azurin
Biophys. J. 2005. 88:4213-4222. [Abstract] [Full Text] [PDF]

Laurent Bozec and Michael Horton

Topography and Mechanical Properties of Single Molecules of Type I Collagen Using Atomic Force Microscopy
Biophys. J. 2005. 88:4223-4231. [Abstract] [Full Text] [PDF]

Connie M. Chung, Jenny D. Chiu, Lawreen H. Connors, Olga Gursky, Amareth Lim, Andrew B. Dykstra, Juris Liepnieks, Merrill D. Benson, Catherine E. Costello, Martha Skinner, and Mary T. Walsh

Thermodynamic Stability of a I Immunoglobulin Light Chain: Relevance to Multiple Myeloma
Biophys. J. 2005. 88:4232-4242. [Abstract] [Full Text] [PDF]

Sharmistha Sinha and Avadhesha Surolia

Oligomerization Endows Enormous Stability to Soybean Agglutinin: A Comparison of the Stability of Monomer and Tetramer of Soybean Agglutinin
Biophys. J. 2005. 88:4243-4251. [Abstract] [Full Text] [PDF]

Kandaswamy Jayachithra, Thallampuranam Krishnaswamy Suresh Kumar, Ta-Jung Lu, Chin Yu, and Der-Hang Chin

Cold Instability of Aponeocarzinostatin and its Stabilization by Labile Chromophore
Biophys. J. 2005. 88:4252-4261. [Abstract] [Full Text] [PDF]

Xing-Hai Chen, Lei Zhang, Yu-Xiang Weng, Lu-Chao Du, Man-Ping Ye, Guo-Zhen Yang, Ritsuko Fujii, Ferdy S. Rondonuwu, Yasushi Koyama, Yi-Shi Wu, and J. P. Zhang

Protein Structural Deformation Induced Lifetime Shortening of Photosynthetic Bacteria Light-Harvesting Complex LH2 Excited State
Biophys. J. 2005. 88:4262-4273. [Abstract] [Full Text] [PDF]

Daniel J. Lacks

Energy Landscape Distortions and the Mechanical Unfolding of Proteins
Biophys. J. 2005. 88:3494-3501. [Abstract] [Full Text] [PDF]

Ana P. S. Citadini, Andressa P. A. Pinto, Ana P. U. Araujo, Otaciro R. Nascimento, and Antonio J. Costa-Filho

EPR Studies of Chlorocatechol 1,2-Dioxygenase: Evidences of Iron Reduction during Catalysis and of the Binding of Amphipatic Molecules
Biophys. J. 2005. 88:3502-3508. [Abstract] [Full Text] [PDF]

Rozeni C. L. Teles, Leonardo de A. Calderon, Francisco J. Medrano, Joao A. R. G. Barbosa, Beatriz G. Guimaraes, Marcelo M. Santoro, and Sonia M. de Freitas

pH Dependence Thermal Stability of a Chymotrypsin Inhibitor from Schizolobium parahyba Seeds
Biophys. J. 2005. 88:3509-3517. [Abstract] [Full Text] [PDF]

Changxia Sun, Jinghe Yang, Xia Wu, Xirong Huang, Fei Wang, and Shufang Liu

Unfolding and Refolding of Bovine Serum Albumin Induced by Cetylpyridinium Bromide
Biophys. J. 2005. 88:3518-3524. [Abstract] [Full Text] [PDF]

Jocelyne Vreede, Wim Crielaard, Klaas J. Hellingwerf, and Peter G. Bolhuis

Predicting the Signaling State of Photoactive Yellow Protein
Biophys. J. 2005. 88:3525-3535. [Abstract] [Full Text] [PDF]

Martin Karlsson and Uno Carlsson

Protein Adsorption Orientation in the Light of Fluorescent Probes: Mapping of the Interaction between Site-Directly Labeled Human Carbonic Anhydrase II and Silica Nanoparticles
Biophys. J. 2005. 88:3536-3544. [Abstract] [Full Text] [PDF]

Paul E. Richardson, Medha Manchekar, Nassrin Dashti, Martin K. Jones, Anne Beigneux, Stephen G. Young, Stephen C. Harvey, and Jere P. Segrest

Assembly of Lipoprotein Particles Containing Apolipoprotein-B: Structural Model for the Nascent Lipoprotein Particle
Biophys. J. 2005. 88:2789-2800. [Abstract] [Full Text] [PDF]

Wei Zhang, John S. Olson, and George N. Phillips Jr.

Biophysical and Kinetic Characterization of HemAT, an Aerotaxis Receptor from Bacillus subtilis
Biophys. J. 2005. 88:2801-2814. [Abstract] [Full Text] [PDF]

Alexey Aprelev, Maria A. Rotter, Zipora Etzion, Robert M. Bookchin, Robin W. Briehl, and Frank A. Ferrone

The Effects of Erythrocyte Membranes on the Nucleation of Sickle Hemoglobin
Biophys. J. 2005. 88:2815-2822. [Abstract] [Full Text] [PDF]

Ingemar von Ossowski, Julian T. Eaton, Mirjam Czjzek, Stephen J. Perkins, Torben P. Frandsen, Martin Schulein, Pierre Panine, Bernard Henrissat, and Veronique Receveur-Brechot

Protein Disorder: Conformational Distribution of the Flexible Linker in a Chimeric Double Cellulase
Biophys. J. 2005. 88:2823-2832. [Abstract] [Full Text] [PDF]

Beining Nie, Jerrod Stutzman, and Aihua Xie

A Vibrational Spectral Maker for Probing the Hydrogen-Bonding Status of Protonated Asp and Glu Residues
Biophys. J. 2005. 88:2833-2847. [Abstract] [Full Text] [PDF]

Christian Boudier, Ann Gils, Paul J. Declerck, and Joseph G. Bieth

The Conversion of Active to Latent Plasminogen Activator Inhibitor-1 Is an Energetically Silent Event
Biophys. J. 2005. 88:2848-2854. [Abstract] [Full Text] [PDF]

Karim Snoussi and Bertil Halle

Protein Self-Association Induced by Macromolecular Crowding: A Quantitative Analysis by Magnetic Relaxation Dispersion
Biophys. J. 2005. 88:2855-2866. [Abstract] [Full Text] [PDF]

Suzanne Scarlata

Determination of the Activation Volume of PLCß by Gß-Subunits through the Use of High Hydrostatic Pressure
Biophys. J. 2005. 88:2867-2874. [Abstract] [Full Text] [PDF]

L. Maragliano, M. Falconi, A. Sergi, P. Cioni, S. Castelli, A. Lania, M. E. Stroppolo, G. Strambini, M. Ferrario, and A. Desideri

Experimental and Simulative Dissociation of Dimeric Cu,Zn Superoxide Dismutase Doubly Mutated at the Intersubunit Surface
Biophys. J. 2005. 88:2875-2882. [Abstract] [Full Text] [PDF]

Peter Werner Hildebrand, Kristian Rother, Andrean Goede, Robert Preissner, and Cornelius Frommel

Molecular Packing and Packing Defects in Helical Membrane Proteins
Biophys. J. 2005. 88:1970-1977. [Abstract] [Full Text] [PDF]

Hartwig Lehle, Jan M. Kriegl, Karin Nienhaus, Pengchi Deng, Stephanus Fengler, and G. Ulrich Nienhaus

Probing Electric Fields in Protein Cavities by Using the Vibrational Stark Effect of Carbon Monoxide
Biophys. J. 2005. 88:1978-1990. [Abstract] [Full Text] [PDF]

Daniele Dell'Orco, Wei-Feng Xue, Eva Thulin, and Sara Linse

Electrostatic Contributions to the Kinetics and Thermodynamics of Protein Assembly
Biophys. J. 2005. 88:1991-2002. [Abstract] [Full Text] [PDF]

Antonello Merlino, Marc Antoine Ceruso, Luigi Vitagliano, and Lelio Mazzarella

Open Interface and Large Quaternary Structure Movements in 3D Domain Swapped Proteins: Insights from Molecular Dynamics Simulations of the C-Terminal Swapped Dimer of Ribonuclease A
Biophys. J. 2005. 88:2003-2012. [Abstract] [Full Text] [PDF]

M. R. H. Krebs, E. H. C. Bromley, S. S. Rogers, and A. M. Donald

The Mechanism of Amyloid Spherulite Formation by Bovine Insulin
Biophys. J. 2005. 88:2013-2021. [Abstract] [Full Text] [PDF]

Ross W. S. Rounsevell, Annette Steward, and Jane Clarke

Biophysical Investigations of Engineered Polyproteins: Implications for Force Data
Biophys. J. 2005. 88:2022-2029. [Abstract] [Full Text] [PDF]

Monika Bokor, Veronika Csizmok, Denes Kovacs, Peter Banki, Peter Friedrich, Peter Tompa, and Kalman Tompa

NMR Relaxation Studies on the Hydrate Layer of Intrinsically Unstructured Proteins
Biophys. J. 2005. 88:2030-2037. [Abstract] [Full Text] [PDF]

Lisa Giachini, Francesco Francia, Antonia Mallardi, Gerardo Palazzo, Emilio Carpene, Federico Boscherini, and Giovanni Venturoli

Multiple Scattering X-Ray Absorption Studies of Zn²⁺ Binding Sites in Bacterial Photosynthetic Reaction Centers
Biophys. J. 2005. 88:2038-2046. [Abstract] [Full Text] [PDF]

Naoyoshi Sakaki, Rieko Shimo-Kon, Kengo Adachi, Hiroyasu Itoh, Shou Furuike, Eiro Muneyuki, Masasuke Yoshida, and Kazuhiko Kinosita Jr.

One Rotary Mechanism for F₁-ATPase over ATP Concentrations from Millimolar down to Nanomolar
Biophys. J. 2005. 88:2047-2056. [Abstract] [Full Text] [PDF]

Qiuying Chen, Iraj Lalezari, Ronald L. Nagel, and Rhoda Elison Hirsch

Liganded Hemoglobin Structural Perturbations by the Allosteric Effector L35
Biophys. J. 2005. 88:2057-2067. [Abstract] [Full Text] [PDF]

Takashi Kamei, Seiji Kakuta, and Hideo Higuchi

Biased Binding of Single Molecules and Continuous Movement of Multiple Molecules of Truncated Single-Headed Kinesin
Biophys. J. 2005. 88:2068-2077. [Abstract] [Full Text] [PDF]

Marjorie Bon Homme, Carol Carter, and Suzanne Scarlata

The Cysteine Residues of HIV-1 Capsid Regulate Oligomerization and Cyclophilin A-Induced Changes
Biophys. J. 2005. 88:2078-2088. [Abstract] [Full Text] [PDF]

Catherine Tetreau, Liliane Mouawad, Samuel Murail, Patricia Duchambon, Yves Blouquit, and Daniel Lavalette

Disentangling Ligand Migration and Heme Pocket Relaxation in Cytochrome P450_cam
Biophys. J. 2005. 88:1250-1263. [Abstract] [Full Text] [PDF]

Cui-Yan Tan, Chun-He Xu, Jun Wong, Jian-Ren Shen, Shinsuke Sakuma, Yasusi Yamamoto, Reinhard Lange, Claude Balny, and Kang-Cheng Ruan

Pressure Equilibrium and Jump Study on Unfolding of 23-kDa Protein from Spinach Photosystem II
Biophys. J. 2005. 88:1264-1275. [Abstract] [Full Text] [PDF]

Dessislava Georgieva, Daniel Schwark, Peter Nikolov, Krassimira Idakieva, Katja Parvanova, Karsten Dierks, Nicolay Genov, and Christian Betzel

Conformational States of the Rapana thomasiana Hemocyanin and Its Substructures Studied by Dynamic Light Scattering and Time-Resolved Fluorescence Spectroscopy
Biophys. J. 2005. 88:1276-1282. [Abstract] [Full Text] [PDF]

Jaume Torres, Jifeng Wang, Krupakar Parthasarathy, and Ding Xiang Liu

The Transmembrane Oligomers of Coronavirus Protein E
Biophys. J. 2005. 88:1283-1290. [Abstract] [Full Text] [PDF]

Alejandra Leo-Macias, Pedro Lopez-Romero, Dmitry Lupyan, Daniel Zerbino, and Angel R. Ortiz

An Analysis of Core Deformations in Protein Superfamilies
Biophys. J. 2005. 88:1291-1299. [Abstract] [Full Text] [PDF]

Sharmistha Sinha, Nivedita Mitra, Gyanendra Kumar, Kanika Bajaj, and Avadhesha Surolia

Unfolding Studies on Soybean Agglutinin and Concanavalin A Tetramers: A Comparative Account
Biophys. J. 2005. 88:1300-1310. [Abstract] [Full Text] [PDF]

Luis A. Campos, Santiago Cuesta-Lopez, Jon Lopez-Llano, Fernando Falo, and Javier Sancho

A Double-Deletion Method to Quantifying Incremental Binding Energies in Proteins from Experiment: Example of a Destabilizing Hydrogen Bonding Pair
Biophys. J. 2005. 88:1311-1321. [Abstract] [Full Text] [PDF]

Ananthakrishnan Sethuraman and Georges Belfort

Protein Structural Perturbation and Aggregation on Homogeneous Surfaces
Biophys. J. 2005. 88:1322-1333. [Abstract] [Full Text] [PDF]

Alessandro Barducci, Riccardo Chelli, Piero Procacci, and Vincenzo Schettino

Misfolding Pathways of the Prion Protein Probed by Molecular Dynamics Simulations
Biophys. J. 2005. 88:1334-1343. [Abstract] [Full Text] [PDF]

Ralf Jansen, Wojciech Dzwolak, and Roland Winter

Amyloidogenic Self-Assembly of Insulin Aggregates Probed by High Resolution Atomic Force Microscopy
Biophys. J. 2005. 88:1344-1353. [Abstract] [Full Text] [PDF]

Peter Bagossi, Gabor Horvath, Gyorgy Vereb, Janos Szollosi, and Jozsef Tozser

Molecular Modeling of Nearly Full-Length ErbB2 Receptor
Biophys. J. 2005. 88:1354-1363. [Abstract] [Full Text] [PDF]

Ken Victor, Alexandra Van-Quynh, and Robert G. Bryant

High Frequency Dynamics in Hemoglobin Measured by Magnetic Relaxation Dispersion
Biophys. J. 2005. 88:443-454. [Abstract] [Full Text] [PDF]

Chi-Yuan Chou, Yi-Ling Lin, Yu-Chyi Huang, Sheh-Yi Sheu, Ta-Hsien Lin, Huey-Jen Tsay, Gu-Gang Chang, and Ming-Shi Shiao

Structural Variation in Human Apolipoprotein E3 and E4: Secondary Structure, Tertiary Structure, and Size Distribution
Biophys. J. 2005. 88:455-466. [Abstract] [Full Text] [PDF]

Sotirios Koutsopoulos, John van der Oost, and Willem Norde

Structural Features of a Hyperthermostable Endo-ß-1,3-glucanase in Solution and Adsorbed on "Invisible" Particles
Biophys. J. 2005. 88:467-474. [Abstract] [Full Text] [PDF]

Curtis W. Sikora and Raymond J. Turner

Investigation of Ligand Binding to the Multidrug Resistance Protein EmrE by Isothermal Titration Calorimetry
Biophys. J. 2005. 88:475-482. [Abstract] [Full Text] [PDF]

Sergio F. Sousa, Pedro A. Fernandes, and Maria Joao Ramos

Farnesyltransferase—New Insights into the Zinc-Coordination Sphere Paradigm: Evidence for a Carboxylate-Shift Mechanism
Biophys. J. 2005. 88:483-494. [Abstract] [Full Text] [PDF]

M. Heuberger, T. Drobek, and N. D. Spencer

Interaction Forces and Morphology of a Protein-Resistant Poly(ethylene glycol) Layer
Biophys. J. 2005. 88:495-504. [Abstract] [Full Text] [PDF]

Vladimir P. Denisov, Jamie L. Schlessman, Bertrand Garcia-Moreno E., and Bertil Halle

Stabilization of Internal Charges in a Protein: Water Penetration or Conformational Change?
Biophys. J. 2004. 87:3982-3994. [Abstract] [Full Text] [PDF]

Chia-Lin Chyan, Fan-Chi Lin, Haibo Peng, Jian-Min Yuan, Chung-Hung Chang, Sheng-Hsien Lin, and Guoliang Yang

Reversible Mechanical Unfolding of Single Ubiquitin Molecules
Biophys. J. 2004. 87:3995-4006. [Abstract] [Full Text] [PDF]

Satoko Ohta, Mohammad Taufiq Alam, Hideo Arakawa, and Atsushi Ikai

Origin of Mechanical Strength of Bovine Carbonic Anhydrase Studied by Molecular Dynamics Simulation
Biophys. J. 2004. 87:4007-4020. [Abstract] [Full Text] [PDF]

Michael Slutsky and Leonid A. Mirny

Kinetics of Protein-DNA Interaction: Facilitated Target Location in Sequence-Dependent Potential
Biophys. J. 2004. 87:4021-4035. [Abstract] [Full Text] [PDF]

Roy W. Alston, Lubica Urbanikova, Jozef Sevcik, Mauricio Lasagna, Gregory D. Reinhart, J. Martin Scholtz, and C. Nick Pace

Contribution of Single Tryptophan Residues to the Fluorescence and Stability of Ribonuclease Sa
Biophys. J. 2004. 87:4036-4047. [Abstract] [Full Text] [PDF]

Harminder Bajaj, Vikas K. Sharma, and Devendra S. Kalonia

Determination of Second Virial Coefficient of Proteins Using a Dual-Detector Cell for Simultaneous Measurement of Scattered Light Intensity and Concentration in SEC-HPLC
Biophys. J. 2004. 87:4048-4055. [Abstract] [Full Text] [PDF]

K. Moncoq, I. Broutin, C. T. Craescu, P. Vachette, A. Ducruix, and D. Durand

SAXS Study of the PIR Domain from the Grb14 Molecular Adaptor: A Natively Unfolded Protein with a Transient Structure Primer?
Biophys. J. 2004. 87:4056-4064. [Abstract] [Full Text] [PDF]

Shixin Ye, Joseph Strzalka, Inna Y. Churbanova, Songyan Zheng, Jonas S. Johansson, and J. Kent Blasie

A Model Membrane Protein for Binding Volatile Anesthetics
Biophys. J. 2004. 87:4065-4074. [Abstract] [Full Text] [PDF]

Marina Gimpelev, Lucy R. Forrest, Diana Murray, and Barry Honig

Helical Packing Patterns in Membrane and Soluble Proteins
Biophys. J. 2004. 87:4075-4086. [Abstract] [Full Text] [PDF]

G. Chillemi, M. Redinbo, A. Bruselles, and A. Desideri

Role of the Linker Domain and the 203–214 N-Terminal Residues in the Human Topoisomerase I DNA Complex Dynamics
Biophys. J. 2004. 87:4087-4097. [Abstract] [Full Text] [PDF]

James D. Lear, Amanda L. Stouffer, Holly Gratkowski, Vikas Nanda, and William F. DeGrado

Association of a Model Transmembrane Peptide Containing Gly in a Heptad Sequence Motif
Biophys. J. 2004. 87:3421-3429. [Abstract] [Full Text] [PDF]

Bernie D. Sattin and M. Cynthia Goh

Direct Observation of the Assembly of RecA/DNA Complexes by Atomic Force Microscopy
Biophys. J. 2004. 87:3430-3436. [Abstract] [Full Text] [PDF]

Kristina Nilsson, Hans-Petter Hersleth, Thomas H. Rod, K. Kristoffer Andersson, and Ulf Ryde

The Protonation Status of Compound II in Myoglobin, Studied by a Combination of Experimental Data and Quantum Chemical Calculations: Quantum Refinement
Biophys. J. 2004. 87:3437-3447. [Abstract] [Full Text] [PDF]

Sarel J. Fleishman, Susan Harrington, Richard A. Friesner, Barry Honig, and Nir Ben-Tal

An Automatic Method for Predicting Transmembrane Protein Structures Using Cryo-EM and Evolutionary Data
Biophys. J. 2004. 87:3448-3459. [Abstract] [Full Text] [PDF]

Aaron K. Chamberlain and James U. Bowie

Analysis of Side-Chain Rotamers in Transmembrane Proteins
Biophys. J. 2004. 87:3460-3469. [Abstract] [Full Text] [PDF]

Xiaohui Zhang, Susan E. Craig, Hishani Kirby, Martin J. Humphries, and Vincent T. Moy

Molecular Basis for the Dynamic Strength of the Integrin ₄ß₁/VCAM-1 Interaction
Biophys. J. 2004. 87:3470-3478. [Abstract] [Full Text] [PDF]

Amit Paliwal, Dilipkumar Asthagiri, Dobrin P. Bossev, and Michael E. Paulaitis

Pressure Denaturation of Staphylococcal Nuclease Studied by Neutron Small-Angle Scat