Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations

被引:8
作者
Galano-Frutos, Juan J. [1 ,2 ]
Nerin-Fonz, Francho [1 ,3 ]
Sancho, Javier [1 ,2 ,4 ]
机构
[1] Univ Zaragoza, Fac Sci, Dept Biochem Mol & Cell Biol, Zaragoza 50009, Spain
[2] Univ Zaragoza, Biocomputat & Complex Syst Phys Inst BIFI, Joint Unit GBs CSIC, Zaragoza 50018, Spain
[3] Acad Athens, Biomed Res Fdn, Athens 11527, Greece
[4] Aragon Hlth Res Inst IIS Aragon, Zaragoza 50009, Spain
关键词
STAPHYLOCOCCAL NUCLEASE; STRUCTURAL-ANALYSIS; FORCE-FIELD; CHYMOTRYPSIN INHIBITOR-2; MUTANT FORMS; BARNASE; STABILITY; APOFLAVODOXIN; SEQUENCE; DENATURATION;
D O I
10.1021/acs.jcim.3c01107
中图分类号
R914 [药物化学];
学科分类号
100701 ;
摘要
Fundamental properties of the Au(111)-KPF6 interface, particularly the potential of zero charge (PZC), exhibit pronounced variations among solvents, yet the origin remains largely elusive. In this study, we aim to link the solvent dependency to the microscopic phenomenon of electron spillover occurring at the metal-solution interface in heterogeneous dielectric media. Addressing the challenge of describing the solvent-modulated electron spillover under constant potential conditions, we adopt a semiclassical functional approach and parametrize it with first-principles calculations and experimental data. We unveil that the key variable governing this phenomenon is the local permittivity within the region approximately 2.5 & Aring; above the metal edge. A higher local permittivity facilitates the electron spillover that tends to increase the PZC on the one hand and enhances the screening of the electronic charge that tends to decrease the PZC on the other. These dual effect lead to a nonmonotonic relationship between the PZC and the local permittivity. Moreover, our findings reveal that the electron spillover induces a capacitance peak at electrode potentials that are more negative than the PZC in concentrated solutions. This observation contrasts classical models predicting the peak to occur precisely at the PZC. To elucidate the contribution of electron spillover to the total capacitance, we decompose the total capacitance into a quantum capacitance of the metal C-q, a classical capacitance of electrolyte solution C-c, and a capacitance C-qc accounting for electron-ion correlations. Our calculations reveal that C-qc is negative due to the promoted electron spillover at more negative potentials. Our work not only reveals the importance of local permittivity in tuning the electron spillover but also presents a viable theoretical approach to study solvent effects on electrochemical interfaces under operating conditions.
引用
收藏
页码:7791 / 7806
页数:16
相关论文
共 111 条
[61]   A DIFFERENTIAL SCANNING CALORIMETRIC STUDY OF THE THERMAL UNFOLDING OF MUTANT FORMS OF PHAGE T4-LYSOZYME [J].
LADBURY, JE ;
HU, CQ ;
STURTEVANT, JM .
BIOCHEMISTRY, 1992, 31 (44) :10699-10702
[62]   Direct examination of the relevance for folding, binding and electron transfer of a conserved protein folding intermediate [J].
Lamazares, Emilio ;
Vega, Sonia ;
Ferreira, Patricia ;
Medina, Milagros ;
Galano-Frutos, Juan J. ;
Martinez-Julvez, Marta ;
Velazquez-Campoy, Adrian ;
Sancho, Javier .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2017, 19 (29) :19021-19031
[63]   Rational stabilization of complex proteins: a divide and combine approach [J].
Lamazares, Emilio ;
Clemente, Isabel ;
Bueno, Marta ;
Velazquez-Campoy, Adrian ;
Sancho, Javier .
SCIENTIFIC REPORTS, 2015, 5
[64]  
Legg M. J., 1982, ProteinData Bank
[65]   Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations [J].
Lei, Hongxing ;
Wu, Chun ;
Liu, Haiguang ;
Duan, Yong .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (12) :4925-4930
[66]   Systematic Validation of Protein Force Fields against Experimental Data [J].
Lindorff-Larsen, Kresten ;
Maragakis, Paul ;
Piana, Stefano ;
Eastwood, Michael P. ;
Dror, Ron O. ;
Shaw, David E. .
PLOS ONE, 2012, 7 (02)
[67]   Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation [J].
Lindorff-Larsen, Kresten ;
Trbovic, Nikola ;
Maragakis, Paul ;
Piana, Stefano ;
Shaw, David E. .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2012, 134 (08) :3787-3791
[68]   How Fast-Folding Proteins Fold [J].
Lindorff-Larsen, Kresten ;
Piana, Stefano ;
Dror, Ron O. ;
Shaw, David E. .
SCIENCE, 2011, 334 (6055) :517-520
[69]   Improved side-chain torsion potentials for the Amber ff99SB protein force field [J].
Lindorff-Larsen, Kresten ;
Piana, Stefano ;
Palmo, Kim ;
Maragakis, Paul ;
Klepeis, John L. ;
Dror, Ron O. ;
shaw, David E. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2010, 78 (08) :1950-1958
[70]   Differential stabilization of the three FMN redox forms by tyrosine 94 and tryptophan 57 in flavodoxin from Anabaena and its influence on the redox potentials? [J].
Lostao, A ;
GomezMoreno, C ;
Mayhew, SG ;
Sancho, J .
BIOCHEMISTRY, 1997, 36 (47) :14334-14344