Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation Study

PLoS Computational Biology - Tập 8 Số 11 - Trang e1002777
Peter M. Kekenes‐Huskey1, Steffen Lindert, J. Andrew McCammon
1Department of Pharmacology, Center for Theoretical Biological Physics, National Computational Biomedical Resource and Howard Hughes Medical Institute, University of California San Diego, La Jolla, California, United States of America

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AMA Gordon, 2000, Regulation of contraction in striated muscle, Physiol Rev, 80, 853, 10.1152/physrev.2000.80.2.853

JCJ Tardiff, 2005, Sarcomeric proteins and familial hypertrophic cardiomyopathy: linking mutations in structural proteins to complex cardiovascular phenotypes, Heart Failure Rev, 10, 237, 10.1007/s10741-005-5253-5

A Gomes, 2005, Mutations in human cardiac Troponin I that are associated with restrictive cardiomyopathy affect basal ATPase activity and the calcium sensitivity of force development, J Biol Chem, 280, 30909, 10.1074/jbc.M500287200

SB Marston, 2011, How Do Mutations in Contractile Proteins Cause the Primary Familial Cardiomyopathies?, J Cardio Trans Res, 4, 245, 10.1007/s12265-011-9266-2

A Kimura, 2010, Molecular basis of hereditary cardiomyopathy: abnormalities in calcium sensitivity, stretch response, stress response and beyond, J Hum Genet, 55, 81, 10.1038/jhg.2009.138

CC Lim, 2008, A novel mutant cardiac troponin C disrupts molecular motions critical for calcium binding affinity and cardiomyocyte contractility, Biophys J, 94, 3577, 10.1529/biophysj.107.112896

Y Li, 2000, Bepridil opens the regulatory N-terminal lobe of cardiac troponin C, Proc Natl Acad Sci, 97, 5140, 10.1073/pnas.090098997

MS Parvatiyar, 2010, Predicting cardiomyopathic phenotypes by altering the Ca2+ affinity of cardiac troponin C, The J Biol Chem, 285, 27785, 10.1074/jbc.M110.112326

J Pinto, 2009, A functional and structural study of troponin C mutations related to hypertrophic cardiomyopathy, The J Biol Chem, 284, 19090, 10.1074/jbc.M109.007021

SB Tikunova, 2004, Designing Calcium-sensitizing Mutations in the Regulatory Domain of Cardiac Troponin C, J Biol Chem, 279, 35341, 10.1074/jbc.M405413200

I Robertson, 2011, Visualizing the principal component of 1 H, 15 N-HSQC NMR spectral changes that reflect protein structural or functional properties: application to troponin C, J Biomol NMR, 51, 115, 10.1007/s10858-011-9546-9

S Takeda, 2003, Structure of the core domain of human cardiac troponin in the Ca2+-saturated form, Nature, 424, 35, 10.1038/nature01780

L Spyracopoulos, 2001, Temperature Dependence of Dynamics and Thermodynamics of the Regulatory Domain of Human Cardiac Troponin C, Biochemistry, 40, 12541, 10.1021/bi010903k

L Spyracopoulos, 1998, Dynamics and Thermodynamics of the Regulatory Domain of Human Cardiac Troponin C in the Apo- and Calcium-Saturated States, Biochemistry, 37, 18032, 10.1021/bi9816960

L Spyracopoulos, 1997, Calcium-Induced Structural Transition in the Regulatory Domain of Human Cardiac Troponin C,, Biochemistry, 36, 12138, 10.1021/bi971223d

S Lindert, 2012, Dynamics and Calcium Association to the N-Terminal Regulatory Domain of Human Cardiac Troponin C: A Multiscale Computational Study, J Phys Chem B, 116, 8449, 10.1021/jp212173f

JF Varughese, 2011, Molecular Dynamics and Docking Studies on Cardiac Troponin C, J Biomol Struct Dyn, 29, 123, 10.1080/07391102.2011.10507378

S Lindert, 2012, Millisecond-timescale simulations of Troponin C, Biophys J

D Wang, 2012, Structural and functional consequences of the cardiac troponin C L48Q Ca2+-sensitizing mutation, Biochemistry, 51, 4473, 10.1021/bi3003007

E Darve, 2001, Calculating free energies using average force, J Chem Phys, 115, 9169, 10.1063/1.1410978

M Oleszczuk, 2010, Solution structure of the regulatory domain of human cardiac troponin C in complex with the switch region of cardiac troponin I and W7: The basis of W7 as an inhibitor of cardiac muscle contraction, J Mol Cell Cardiol, 48, 925, 10.1016/j.yjmcc.2010.01.016

SMS Gagn'e, 1998, The NMR angle on troponin C, Biochem Cell Biol, 76, 302, 10.1139/o98-055

A Wand, 2001, Dynamic activation of protein function: a view emerging from NMR spectroscopy, Nat Struct Mol Biol, 8, 926, 10.1038/nsb1101-926

MS Marlow, 2010, The role of conformational entropy in molecular recognition by calmodulin, Nat Chem Biol, 6, 352, 10.1038/nchembio.347

DW Li, 2010, Entropy Localization in Proteins, J Phys Chem B, 114, 16036, 10.1021/jp109908u

R Alsallaq, 2008, Electrostatic rate enhancement and transient complex of proteinprotein association, Prot Func Bioinformatics, 71, 320, 10.1002/prot.21679

Y Ogawa, 1985, Calcium binding to troponin C and troponin: effects of Mg2+, ionic strength and pH, J Biochem, 97, 1011, 10.1093/oxfordjournals.jbchem.a135143

AL Hazard, 1998, The kinetic cycle of cardiac troponin C: Calcium binding and dissociation at site II trigger slow conformational rearrangements, Prot Sci, 7, 2451, 10.1002/pro.5560071123

JP Konhilas, 2001, Myofilament Calcium Sensitivity in Skinned Rat Cardiac Trabeculae: Role of Interfilament Spacing, Circ Res, 90, 59, 10.1161/hh0102.102269

S Tikunova, 2002, Effect of hydrophobic residue substitutions with glutamine on Ca2+ binding and exchange with the N-domain of troponin C, Biochemistry, 41, 6697, 10.1021/bi011763h

FC BERNSTEIN, 1977, The Protein Data Bank. A Computer-Based Archival File for Macromolecular Structures, Eur J Biochem, 80, 319, 10.1111/j.1432-1033.1977.tb11885.x

W Humphrey, 1996, VMD: visual molecular dynamics, J Mol Graphics, 14, 33, 10.1016/0263-7855(96)00018-5

BR Brooks, 2009, CHARMM: The biomolecular simulation program, J Comp Chem, 30, 1545, 10.1002/jcc.21287

J Phillips, 2005, Scalable molecular dynamics with NAMD, J Comp Chem, 26, 1781, 10.1002/jcc.20289

B Dickson, 2010, Free energy calculations: An efficient adaptive biasing potential method, J Phys Chem B, 114, 5823, 10.1021/jp100926h

BJ Grant, 2006, Bio3d: an R package for the comparative analysis of protein structures, Bioinformatics, 22, 2695, 10.1093/bioinformatics/btl461

MM Christen, 2005, The GROMOS software for biomolecular simulation: GROMOS05, J Comp Chem, 26, 1719, 10.1002/jcc.20303

WW Kabsch, 1983, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, 22, 2577, 10.1002/bip.360221211

KLK Yap, 2002, Vector geometry mapping. A method to characterize the conformation of helix-loop-helix calcium-binding proteins, Methods Mol Biol, 173, 317

NA Baker, 2001, Electrostatics of nanosystems: Application to microtubules and the ribosome, Proc Natl Acad Sci U S A, 98, 10037, 10.1073/pnas.181342398

JJ Prompers, 2002, General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation, J Am Chem Soc, 124, 4522, 10.1021/ja012750u

GA Huber, 2010, Browndye: A Software Package for Brownian Dynamics, Comput Phys Commun, 181, 1896, 10.1016/j.cpc.2010.07.022

TJ Dolinsky, 2007, PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations, Nucleic Acids Res, 35, W522, 10.1093/nar/gkm276