Tanford-Kirkwood electrostatics for protein modeling.

نویسندگان

  • J J Havranek
  • P B Harbury
چکیده

Solvent plays a significant role in determining the electrostatic potential energy of proteins, most notably through its favorable interactions with charged residues and its screening of electrostatic interactions. These energetic contributions are frequently ignored in computational protein design and protein modeling methodologies because they are difficult to evaluate rapidly and accurately. To address this deficiency, we report a revised form of the original Tanford-Kirkwood continuum electrostatic model [Tanford, C. & Kirkwood, J. G. (1957) J. Am. Chem. Soc. 79, 5333-5339], which accounts for the effects of solvent polarization on charged atoms in proteins. The Tanford-Kirkwood model was modified to increase its speed and to improve its sensitivity to the details of protein structure. For the 37 electrostatic self-energies of the polar side-chains in bovine pancreatic trypsin inhibitor, and their 666 interaction energies, the modified Tanford-Kirkwood potential of mean force differs from a computationally intensive numerical potential (DelPhi) by root-mean-square errors of 0.6 kcal/mol and 0.08 kcal/mol, respectively. The Tanford-Kirkwood approach makes possible a realistic treatment of electrostatics in computationally demanding protein modeling calculations. For example, pH titration calculations for ovomucoid third domain that model polar side-chain relaxation (including >2 x 10(23) rotamer conformations of the protein) provide pKa values of unprecedented accuracy.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Protein-solvent interactions.

The central importance of solvent interactions in stabilization of specific protein structure has long been recognized. Decades ago, Tanford and Kirkwood treated in detail the interaction of charges with solvent, and they showed how desolvation/burial of charges upon protein folding was an important factor in stability.1 The influence of their model, with further elaborations, can still be seen...

متن کامل

Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum.

The generalized Born (GB) model of continuum electrostatics is an analytic approximation to the Poisson equation useful for predicting the electrostatic component of the solvation free energy for solutes ranging in size from small organic molecules to large macromolecular complexes. This work presents a new continuum electrostatics model based on Kirkwood's analytic result for the electrostatic...

متن کامل

Electrostatic effects on the kinetics of oxidation-reduction reactions of c-type cytochromes.

The kinetics of the oxidation-reduction reactions between horse heart cytochrome c, Euglena gracilis cytochrome c552, and ions (ascorbate, ferricyanide, and ferrocyanide) was investigated as a function of ionic strength at pH 7, 25 degrees C. The ionic strength was varied between 0.002 and 0.02 M. Data were analyzed according to four different functions of ionic strength. Results showed that th...

متن کامل

pH titration of native and unfolded ß-trypsin: evaluation of the ∆∆G0 titration and the carboxyl pK values

The stabilizing free energy of ß-trypsin was determined by hydrogen ion titration. In the pH range from 3.0 to 7.0, the change in free energy difference for the stabilization of the native protein relative to the unfolded one (∆∆G0 titration) was 9.51 ± 0.06 kcal/mol. An isoelectric point of 10.0 was determined, allowing us to calculate the Tanford and Kirkwood electrostatic factor w. This fact...

متن کامل

A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules

We present a treecode-accelerated boundary integral (TABI) solver for electrostatics of solvated biomolecules described by the linear Poisson-Boltzmann equation. The method employs a wellconditioned boundary integral formulation for the electrostatic potential and its normal derivative on the molecular surface. The surface is triangulated and the integral equations are discretized by centroid c...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • Proceedings of the National Academy of Sciences of the United States of America

دوره 96 20  شماره 

صفحات  -

تاریخ انتشار 1999