Electrostatic Solvation Energy for Two Oppositely Charged Ions in a Solvated Protein System: Salt Bridges Can Stabilize Proteins

被引:21
作者
Gong, Haipeng [1 ]
Freed, Karl F. [2 ,3 ]
机构
[1] Tsinghua Univ, Sch Life Sci, Inst Bioinformat & Syst Biol, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China
[2] Univ Chicago, Dept Chem, Chicago, IL 60637 USA
[3] Univ Chicago, James Franck Inst, Chicago, IL 60637 USA
基金
美国国家卫生研究院;
关键词
GENERALIZED BORN APPROXIMATION; DIELECTRIC-CONSTANTS; IMPLICIT SOLVENT; EXPLICIT SOLVENT; MODEL; WATER; LANDSCAPE; DYNAMICS; SURFACE; EQUILIBRIA;
D O I
10.1016/j.bpj.2009.10.031
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
Born-type electrostatic continuum methods have been an indispensable ingredient in a variety of implicit-solvent methods that reduce computational effort by orders of magnitude compared to explicit-solvent MD simulations and thus enable treatment using larger systems and/or longer times. An analysis of the limitations and failures of the Born approaches serves as a guide for fundamental improvements without diminishing the importance of prior works. One of the major limitations of the Born theory is the lack of a liquidlike description of the response of solvent dipoles to the electrostatic field of the solute and the changes therein, a feature contained in the continuum Langevin-Debye (LD) model applied here to investigate how Coulombic interactions depend on the location of charges relative to the protein/water boundary. This physically more realistic LD model is applied to study the stability of salt bridges. When compared head to head using the same (independently measurable) physical parameters (radii, dielectric constants, etc.), the LD model is in good agreement with observations, whereas the Born model is grossly in error. Our calculations also suggest that a salt bridge on the protein's surface can be stabilizing when the charge separation is <= 4 angstrom.
引用
收藏
页码:470 / 477
页数:8
相关论文
共 49 条
[1]   Energetics of the interaction between water and the helical peptide group and its role in determining helix propensities [J].
Avbelj, F ;
Luo, PZ ;
Baldwin, RL .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (20) :10786-10791
[2]   ION-PAIRS IN PROTEINS [J].
BARLOW, DJ ;
THORNTON, JM .
JOURNAL OF MOLECULAR BIOLOGY, 1983, 168 (04) :867-885
[3]   Kinetics of the coil-to-helix transition on a rough energy landscape [J].
Baumketner, A ;
Shea, JE .
PHYSICAL REVIEW E, 2003, 68 (05)
[4]   Protein stabilization by salt bridges: concepts, experimental approaches and clarification of some misunderstandings [J].
Bosshard, HR ;
Marti, DN ;
Jelesarov, I .
JOURNAL OF MOLECULAR RECOGNITION, 2004, 17 (01) :1-16
[5]   ANALYSIS OF THE BORN MODEL FOR HYDRATION OF IONS [J].
BUCHER, M ;
PORTER, TL .
JOURNAL OF PHYSICAL CHEMISTRY, 1986, 90 (15) :3406-3411
[6]   Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models [J].
Bursulaya, BD ;
Brooks, CL .
JOURNAL OF PHYSICAL CHEMISTRY B, 2000, 104 (51) :12378-12383
[7]   Implicit solvation models: Equilibria, structure, spectra, and dynamics [J].
Cramer, CJ ;
Truhlar, DG .
CHEMICAL REVIEWS, 1999, 99 (08) :2161-2200
[8]   The inter-ionic attraction theory of ionized solutes. IV. The influence of variation of dielectric constant on the limiting law for small concentrations [J].
Debye, P ;
Pauling, L .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1925, 47 :2129-2134
[9]  
Debye P., 1929, Polar Molecules
[10]   THEORY FOR THE FOLDING AND STABILITY OF GLOBULAR-PROTEINS [J].
DILL, KA .
BIOCHEMISTRY, 1985, 24 (06) :1501-1509