Fully quantum mechanical description of proteins in solution. Combining linear scaling quantum mechanical methodologies with the Poisson-Boltzmann equation

被引:88
作者
Gogonea, V [1 ]
Merz, KM [1 ]
机构
[1] Penn State Univ, Dept Chem, Davey Lab 152, University Pk, PA 16802 USA
关键词
D O I
10.1021/jp990266w
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
In this paper we report a method for solving the Schrodinger equation for large molecules in solution which involved merging a linear scaling divide and conquer (D&C) semiempirical algorithm with the Poisson-Boltzmann (PB) equation. We then assess the performance of our self-consistent reaction field (SCRF) approach by comparing our D&C-PB calculations for a set of 29 neutral and 36 charged molecules with those obtained by ab initio GVB and DFT (B3LYP) methods, Cramer and Truhlar's semiempirical generalized-Born SM5 model, and with the experimental solvation free energies. Furthermore, we show that our SCRF method can be used to perform fully quantum mechanical calculations of proteins in solution in a reasonable amount of time on a modern workstation. We believe that all electrostatic interactions in biological systems require a quantum mechanical description in order to obtain an accurate representation. Thus, our new SCRF method should have an impact on the computational study of physical and chemical phenomena occurring in proteins and nucleic acids, which are, in general, strongly influenced by electrostatic interactions. Moreover, this may lead to novel insights into classic problems like protein folding or drug design.
引用
收藏
页码:5171 / 5188
页数:18
相关论文
共 113 条
[1]   A SELF-CONSISTENT REACTION FIELD APPROACH TO LIQUID PHOTOIONIZATION [J].
AGREN, H ;
LLANOS, CM ;
MIKKELSEN, KV .
CHEMICAL PHYSICS, 1987, 115 (01) :43-55
[2]   SOLUTIONS OF THE FULL POISSON-BOLTZMANN EQUATION WITH APPLICATION TO DIFFUSION-CONTROLLED REACTIONS [J].
ALLISON, SA ;
SINES, JJ ;
WIERZBICKI, A .
JOURNAL OF PHYSICAL CHEMISTRY, 1989, 93 (15) :5819-5823
[3]  
[Anonymous], JAG 3 5
[4]   A new definition of cavities for the computation of solvation free energies by the polarizable continuum model [J].
Barone, V ;
Cossi, M ;
Tomasi, J .
JOURNAL OF CHEMICAL PHYSICS, 1997, 107 (08) :3210-3221
[5]   FREE-ENERGY CALCULATIONS BY COMPUTER-SIMULATION [J].
BASH, PA ;
SINGH, UC ;
LANGRIDGE, R ;
KOLLMAN, PA .
SCIENCE, 1987, 236 (4801) :564-568
[6]   A WELL-BEHAVED ELECTROSTATIC POTENTIAL BASED METHOD USING CHARGE RESTRAINTS FOR DERIVING ATOMIC CHARGES - THE RESP MODEL [J].
BAYLY, CI ;
CIEPLAK, P ;
CORNELL, WD ;
KOLLMAN, PA .
JOURNAL OF PHYSICAL CHEMISTRY, 1993, 97 (40) :10269-10280
[7]   ATOMIC CHARGES DERIVED FROM SEMIEMPIRICAL METHODS [J].
BESLER, BH ;
MERZ, KM ;
KOLLMAN, PA .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1990, 11 (04) :431-439
[8]   GRID POSITIONING INDEPENDENCE AND THE REDUCTION OF SELF-ENERGY IN THE SOLUTION OF THE POISSON-BOLTZMANN EQUATION [J].
BRUCCOLERI, RE .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1993, 14 (12) :1417-1422
[9]  
Bruccoleri RE, 1997, J COMPUT CHEM, V18, P268, DOI 10.1002/(SICI)1096-987X(19970130)18:2<268::AID-JCC11>3.0.CO
[10]  
2-E