Correlated motions are a fundamental property of β-sheets

Correlated motions in proteins can mediate fundamental biochemical processes such as signal transduction and allostery. The mechanisms that underlie these processes remain largely unknown due mainly to limitations in their direct detection. Here, based on a detailed analysis of protein structures deposited in the protein data bank, as well as on state-of-the art molecular simulations, we provide general evidence for the transfer of structural information by correlated backbone motions, mediated by hydrogen bonds, across β-sheets. We also show that the observed local and long-range correlated motions are mediated by the collective motions of β-sheets and investigate their role in large-scale conformational changes. Correlated motions represent a fundamental property of β-sheets that contributes to protein function.

[1]  Ned S Wingreen,et al.  Flexibility of β‐sheets: Principal component analysis of database protein structures , 2003, Proteins.

[2]  Beat Vögeli,et al.  Comprehensive description of NMR cross-correlated relaxation under anisotropic molecular tumbling and correlated local dynamics on all time scales. , 2010, The Journal of chemical physics.

[3]  Mark Gerstein,et al.  The Database of Macromolecular Motions: new features added at the decade mark , 2005, Nucleic Acids Res..

[4]  Masaki Sasai,et al.  Entropic mechanism of large fluctuation in allosteric transition , 2010, Proceedings of the National Academy of Sciences.

[5]  Erik Lindahl,et al.  Normal-Mode Analysis of the Glycine Alpha1 Receptor by Three Separate Methods , 2007, J. Chem. Inf. Model..

[6]  Jens Meiler,et al.  Side-chain orientation and hydrogen-bonding imprint supra-Tau(c) motion on the protein backbone of ubiquitin. , 2005, Angewandte Chemie.

[7]  David J. Osguthorpe,et al.  Low Frequency Motion in Proteins , 1999 .

[8]  Jianpeng Ma,et al.  CHARMM: The biomolecular simulation program , 2009, J. Comput. Chem..

[9]  D. Kern,et al.  Hidden alternate structures of proline isomerase essential for catalysis , 2010 .

[10]  Ad Bax,et al.  Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. , 2003, Journal of the American Chemical Society.

[11]  Elizabeth J. Denning,et al.  Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions. , 2009, Journal of molecular biology.

[12]  D. Case,et al.  Exploring protein native states and large‐scale conformational changes with a modified generalized born model , 2004, Proteins.

[13]  A Kitao,et al.  Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space. , 1994, Biophysical chemistry.

[14]  Roland L. Dunbrack,et al.  Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains , 1994, Nature Structural Biology.

[15]  Paul M. G. Curmi,et al.  Twist and Shear in bSheets and b-Ribbons , 2022 .

[16]  H. Ng,et al.  Automated electron‐density sampling reveals widespread conformational polymorphism in proteins , 2010, Protein science : a publication of the Protein Society.

[17]  Xavier Salvatella,et al.  Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles , 2011, European Biophysics Journal.

[18]  R. Jernigan,et al.  Anisotropy of fluctuation dynamics of proteins with an elastic network model. , 2001, Biophysical journal.

[19]  Modesto Orozco,et al.  Approaching Elastic Network Models to Molecular Dynamics Flexibility. , 2010, Journal of chemical theory and computation.

[20]  Sean X. Sun,et al.  Elastic energy storage in beta-sheets with application to F1-ATPase. , 2003, European biophysics journal : EBJ.

[21]  Kay Diederichs,et al.  Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose , 1998, Nature Structural Biology.

[22]  M. Hennig,et al.  Direct measurement of angles between bond vectors in high-resolution NMR. , 1997, Science.

[23]  Paul M. G. Curmi,et al.  Twist and shear in β-sheets and β-ribbons , 2002 .

[24]  Rafael Brüschweiler,et al.  Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[25]  James E. Fitzgerald,et al.  Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors. , 2007, Biochemistry.

[26]  P. Chacón,et al.  Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. , 2007, Structure.

[27]  Ian W. Davis,et al.  The backrub motion: how protein backbone shrugs when a sidechain dances. , 2006, Structure.

[28]  G. Marius Clore,et al.  Amplitudes of Protein Backbone Dynamics and Correlated Motions in a Small α/β Protein: Correspondence of Dipolar Coupling and Heteronuclear Relaxation Measurements† , 2004 .

[29]  Henry van den Bedem,et al.  Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR , 2014, Proceedings of the National Academy of Sciences.

[30]  S. Grzesiek,et al.  Ultrahigh-resolution backbone structure of perdeuterated protein GB1 using residual dipolar couplings from two alignment media. , 2006, Angewandte Chemie.

[31]  Piotr Cieplak,et al.  Allosteric transition and binding of small molecule effectors causes curvature change in central β-sheets of selected enzymes , 2011, Journal of molecular modeling.

[32]  F. J. Luque,et al.  Theoretical analysis of antisense duplexes: determinants of the RNase H susceptibility. , 2008, Journal of the American Chemical Society.

[33]  R. Nussinov,et al.  Is allostery an intrinsic property of all dynamic proteins? , 2004, Proteins.

[34]  Sean X. Sun,et al.  Bending elasticity of anti-parallel beta-sheets. , 2007, Biophysical journal.

[35]  Modesto Orozco,et al.  MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories. , 2010, Structure.

[36]  E. Lindahl,et al.  Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models. , 2010, Journal of chemical theory and computation.

[37]  Qiang Cui,et al.  Interpreting correlated motions using normal mode analysis. , 2006, Structure.

[38]  Steven Hayward,et al.  Normal modes and essential dynamics. , 2008, Methods in molecular biology.

[39]  A Kitao,et al.  Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis , 1994, Protein science : a publication of the Protein Society.

[40]  Y. Sanejouand,et al.  Discrete breathers in protein structures , 2008, Physical biology.

[41]  Peter Güntert,et al.  Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs , 2012, Nature Structural &Molecular Biology.

[42]  Luciana Esposito,et al.  Correlation between ω and ψ Dihedral Angles in Protein Structures , 2005 .

[43]  Karsten Suhre,et al.  ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement , 2004, Nucleic Acids Res..

[44]  G T Montelione,et al.  Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-α transforming growth factor , 1995, Journal of biomolecular NMR.

[45]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[46]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[47]  Jeffrey Skolnick,et al.  Fast procedure for reconstruction of full‐atom protein models from reduced representations , 2008, J. Comput. Chem..

[48]  Charles A Laughton,et al.  Fast Atomistic Molecular Dynamics Simulations from Essential Dynamics Samplings. , 2012, Journal of chemical theory and computation.

[49]  A. E. Sitnitsky Dynamical contribution into enzyme catalytic efficiency , 2006, cond-mat/0601165.

[50]  David J. Osguthorpe,et al.  Low Frequency Motion in Proteins Comparison of Normal Mode and Molecular Dynamics of Streptomyces Griseus Protease A , 1999 .

[51]  M. Orozco,et al.  Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations. , 2012, Journal of chemical theory and computation.

[52]  P. Wright,et al.  NMR Order Parameters of Biomolecules: A New Analytical Representation and Application to the Gaussian Axial Fluctuation Model , 1994 .

[53]  R. Brüschweiler,et al.  Short-range coherence of internal protein dynamics revealed by high-precision in silico study. , 2009, Journal of the American Chemical Society.

[54]  H. V. D. Bedem,et al.  Automated identification of functional dynamic contact networks from X-ray crystallography , 2013 .

[55]  Dennis R Livesay,et al.  New insight into long‐range nonadditivity within protein double‐mutant cycles , 2008, Proteins.

[56]  Pablo Chacón,et al.  iMod: multipurpose normal mode analysis in internal coordinates , 2011, Bioinform..

[57]  S. R. Jammalamadaka,et al.  Topics in Circular Statistics , 2001 .

[58]  A. Bax,et al.  Protein backbone motions viewed by intraresidue and sequential HN–Hα residual dipolar couplings , 2008, Journal of biomolecular NMR.

[59]  Phillip L. Geissler,et al.  Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone , 2011, PLoS Comput. Biol..

[60]  X. Salvatella,et al.  Weak Long-Range Correlated Motions in a Surface Patch of Ubiquitin Involved in Molecular Recognition , 2011, Journal of the American Chemical Society.