Multiscale modeling of a conditionally disordered pH-sensing chaperone.

[1]  J. Wyman,et al.  LINKED FUNCTIONS AND RECIPROCAL EFFECTS IN HEMOGLOBIN: A SECOND LOOK. , 1964, Advances in protein chemistry.

[2]  Charles Tanford,et al.  [84] Examination of titration behavior , 1967 .

[3]  C. Tanford Protein denaturation. , 1968, Advances in protein chemistry.

[4]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[5]  R. Swendsen,et al.  THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .

[6]  David W. Capson,et al.  Selection of partitions from a hierarchy , 1993, Pattern Recognit. Lett..

[7]  R. Jernigan,et al.  Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. , 1996, Journal of molecular biology.

[8]  C. Brooks,et al.  Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist β-barrel model , 1998 .

[9]  Fan Yang,et al.  Crystal structure of Escherichia coli HdeA , 1998, Nature Structural Biology.

[10]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[11]  Y. Sugita,et al.  Replica-exchange molecular dynamics method for protein folding , 1999 .

[12]  W. C. Johnson,et al.  Analyzing protein circular dichroism spectra for accurate secondary structures , 1999, Proteins.

[13]  K. Gajiwala,et al.  HDEA, a periplasmic protein that supports acid resistance in pathogenic enteric bacteria. , 2000, Journal of molecular biology.

[14]  P. van Gelder,et al.  Structure and function of bacterial outer membrane proteins: barrels in a nutshell , 2000, Molecular microbiology.

[15]  John Karanicolas,et al.  The origins of asymmetry in the folding transition states of protein L and protein G , 2002, Protein science : a publication of the Protein Society.

[16]  Gary L Gilliland,et al.  Crystal structure of Escherichia coli protein ybgI, a toroidal structure with a dinuclear metal site , 2003 .

[17]  Charles L. Brooks,et al.  Generalized born model with a simple smoothing function , 2003, J. Comput. Chem..

[18]  Michael Feig,et al.  MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. , 2004, Journal of molecular graphics & modelling.

[19]  C. Brooks,et al.  Constant‐pH molecular dynamics using continuous titration coordinates , 2004, Proteins.

[20]  John W. Foster,et al.  Escherichia coli acid resistance: tales of an amateur acidophile , 2004, Nature Reviews Microbiology.

[21]  John W. Foster,et al.  Escherichia coli Glutamate- and Arginine-Dependent Acid Resistance Systems Increase Internal pH and Reverse Transmembrane Potential , 2004, Journal of bacteriology.

[22]  John Mongan,et al.  Biomolecular simulations at constant pH. , 2005, Current opinion in structural biology.

[23]  Weizhe Hong,et al.  Periplasmic Protein HdeA Exhibits Chaperone-like Activity Exclusively within Stomach pH Range by Transforming into Disordered Conformation* , 2005, Journal of Biological Chemistry.

[24]  C. Brooks,et al.  Constant pH molecular dynamics with proton tautomerism. , 2005, Biophysical journal.

[25]  Pinak Chakrabarti,et al.  Macromolecular recognition in the Protein Data Bank , 2006, Acta crystallographica. Section D, Biological crystallography.

[26]  S. Milles,et al.  Solubilization of Protein Aggregates by the Acid Stress Chaperones HdeA and HdeB* , 2008, Journal of Biological Chemistry.

[27]  Gerhard Hummer,et al.  Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. , 2008, Journal of molecular biology.

[28]  Charles L Brooks,et al.  Recent advances in implicit solvent-based methods for biomolecular simulations. , 2008, Current opinion in structural biology.

[29]  H. Chan,et al.  Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding , 2008, Proceedings of the National Academy of Sciences.

[30]  Yaakov Levy,et al.  Nonnative electrostatic interactions can modulate protein folding: molecular dynamics with a grain of salt. , 2009, Journal of molecular biology.

[31]  E. Vierling,et al.  Substrate binding site flexibility of the small heat shock protein molecular chaperones , 2009, Proceedings of the National Academy of Sciences.

[32]  Titus M. Franzmann,et al.  Protein refolding by pH-triggered chaperone binding and release , 2009, Proceedings of the National Academy of Sciences.

[33]  Roland L. Dunbrack,et al.  proteins STRUCTURE O FUNCTION O BIOINFORMATICS Improved prediction of protein side-chain conformations with SCWRL4 , 2022 .

[34]  U. Jakob,et al.  Structural plasticity of an acid-activated chaperone allows promiscuous substrate binding , 2009, Proceedings of the National Academy of Sciences.

[35]  Debabani Ganguly,et al.  Topology‐based modeling of intrinsically disordered proteins: Balancing intrinsic folding and intermolecular interactions , 2011, Proteins.

[36]  Jana K. Shen,et al.  Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy , 2011, Proteins.

[37]  Peng R. Chen,et al.  A genetically incorporated crosslinker reveals chaperone cooperation in acid resistance. , 2011, Nature chemical biology.

[38]  Lucia Brunetti,et al.  Probing pH-dependent dissociation of HdeA dimers. , 2011, Journal of the American Chemical Society.

[39]  Damien Farrell,et al.  Remeasuring HEWL pKa values by NMR spectroscopy: Methods, analysis, accuracy, and implications for theoretical pKa calculations , 2011, Proteins.

[40]  R. Best,et al.  Modulation of an IDP binding mechanism and rates by helix propensity and non-native interactions: association of HIF1α with CBP. , 2012, Molecular bioSystems.

[41]  U. Jakob,et al.  Conditional disorder in chaperone action. , 2012, Trends in biochemical sciences.

[42]  Jianhan Chen,et al.  Electrostatically accelerated coupled binding and folding of intrinsically disordered proteins. , 2012, Journal of molecular biology.

[43]  Weizhe Hong,et al.  Chaperone-dependent mechanisms for acid resistance in enteric bacteria. , 2012, Trends in microbiology.

[44]  D. Thirumalai,et al.  Effects of pH on proteins: predictions for ensemble and single-molecule pulling experiments. , 2012, Journal of the American Chemical Society.

[45]  Roni Mittelman,et al.  Order out of Disorder: Working Cycle of an Intrinsically Unfolded Chaperone , 2012, Cell.

[46]  Weihong Zhang,et al.  Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins , 2013, PLoS Comput. Biol..

[47]  Alex Dickson,et al.  Binding and folding of the small bacterial chaperone HdeA. , 2013, The journal of physical chemistry. B.

[48]  C. Brooks,et al.  Chaperone activation by unfolding , 2013, Proceedings of the National Academy of Sciences.

[49]  How bacteria survive an acid trip , 2013, Proceedings of the National Academy of Sciences.

[50]  Jessica K. Gagnon,et al.  Prepaying the entropic cost for allosteric regulation in KIX , 2014, Proceedings of the National Academy of Sciences.

[51]  Logan S. Ahlstrom,et al.  Hamiltonian Mapping Revisited: Calibrating Minimalist Models to Capture Molecular Recognition by Intrinsically Disordered Proteins , 2014, The journal of physical chemistry letters.

[52]  Loïc Salmon,et al.  HdeB Functions as an Acid-protective Chaperone in Bacteria* , 2014, The Journal of Biological Chemistry.

[53]  K. Crowhurst,et al.  NMR‐monitored titration of acid‐stress bacterial chaperone HdeA reveals that Asp and Glu charge neutralization produces a loosened dimer structure in preparation for protein unfolding and chaperone activation , 2014, Protein science : a publication of the Protein Society.