Search PubMed⌕ Search

Biomedical subjects

M K Gilson

Publications and source records attributed to M K Gilson.

29 records · Page 2Linked to original sources
PubMed1994

Open "back door" in a molecular dynamics simulation of acetylcholinesterase.

The enzyme acetylcholinesterase generates a strong electrostatic field that can attract the cationic substrate acetylcholine to the active site. However, the long and narrow active site gorge seems inconsistent with the enzyme's high catalytic rate. A molecular dynamics simulation of acetylcholinesterase in water reveals the transient opening of a short channel, large enough to pass a water molecule, through a thin wall of the active site near tryptophan-84. This simulation suggests that substrate, products, or solvent could move through this "back door," in addition to the entrance revealed by the crystallographic structure. Electrostatic calculations show a strong field at the back door, oriented to attract the substrate and the reaction product choline and to repel the other reaction product, acetate. Analysis of the open back door conformation suggests a mutation that could seal the back door and thus test the hypothesis that thermal motion of this enzyme may open multiple routes of access to its active site.

Acetylcholine↗
PubMed1993

Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins.

Computer models of proteins frequently treat the energies and forces associated with ionizable groups as if they were purely electrostatic. This paper examines the validity of the purely electrostatic approach, and concludes that significant errors in energies can result from the neglect of ionization changes. However, a complete treatment of ionizable groups presents substantial computational obstacles, because of the large number of ionization states which must be examined in systems having multiple interacting titratable groups. In order to address this problem, two novel methods for treating the energetics and forces associated with ionizable groups with a minimum of computer time have been developed. The most rapid method yields approximate energies by computing the free energy of a single highly occupied ionization state. The second method separates ionizable groups into clusters, and treats intracluster interactions exactly, but intercluster interactions approximately. This method yields both accurate energies and fractional charges. Good results are obtained in tests of both methods on proteins having has many as 123 ionizable groups. The more rapid method requires computer times of 0.01 to 0.34 sec, while the more accurate method requires 0.7 to 15 sec. These methods may be fast enough to permit the incorporation of ionization effects in iterative computations, such as energy minimizations and conformational searches.

Animals↗
PubMed1991

The inclusion of electrostatic hydration energies in molecular mechanics calculations.

The problem of including solvent effects in molecular mechanics calculations is discussed. It is argued that the neglect of charge-solvent (solvation) interactions can introduce significant errors. The finite difference Poisson-Boltzmann (FDPB) method for calculating electrostatic interactions is summarized and is used as a basis for introducing a new pairwise energy term which accounts for charge-solvent interactions. This term acts between all pairs of atoms usually considered in molecular mechanics calculations and can be easily incorporated into existing force fields. As an example, a parameterization is developed for the CHARMm force field and the results compared to the predictions of the FDPB method. An approach to the realistic incorporation of solvent screening into force fields is also outlined.

Chemical Phenomena↗
PubMed1989

Destabilization of an alpha-helix-bundle protein by helix dipoles.

The finite difference Poisson-Boltzmann method is used to calculate the electrostatic work of assembling the four alpha-helices of Themiste dyscritum hemerythrin to form the protein's observed antiparallel helical bundle. The calculations account for the interaction of each helix dipole with the high-dielectric solvent as well as for pairwise interactions of the dipoles with each other. We find that the electrostatic work of assembly is dominated by unfavorable changes in dipole-solvent interactions rather than by favorable interactions between antiparallel helices. Furthermore, the electrostatic energy difference between the observed arrangement of helices in hemerythrin and at least one other possible helical arrangement is less than 1 kT. These results suggest that the helix dipole actually destabilizes the helical bundle and that it plays little or no role in producing the observed bundle geometry.

Calorimetry↗
PubMed1988

Energetics of charge-charge interactions in proteins.

Electrostatic interactions between pairs of atoms in proteins are calculated with a model based on the linearized Poisson-Boltzmann equation. The equation is solved accurately by a method that takes into account the detailed shape of the protein. This paper presents applications to several systems. Experimental data for the interaction of ionized residues with an active site histidine in subtilisin BPN' allow the model to be tested, using various assumptions for the electrical properties of the protein and solvent. The electrostatic stabilization of the active site thiolate of rhodanese is analyzed, with attention to the influence of alpha-helices. Finally, relationships between electrostatic potential and charge-charge distance are reported for large and small globular proteins. The above results are compared with those of simpler electrostatic models, including Coulomb's law with both a distance-dependent dielectric constant (epsilon = R) and a fixed dielectric constant (epsilon = 2), and Tanford-Kirkwood theory. The primary conclusions are as follows: 1) The Poisson-Boltzmann model agrees with the subtilisin data over a range of ionic strengths; 2) two alpha-helices generate a large potential in the active site of rhodanese; 3) epsilon = R overestimates weak electrostatic interactions but yields relatively good results for strong ones; 4) Tanford-Kirkwood theory is a useful approximation to detailed solutions of the linearized Poisson-Boltzmann equation in globular proteins; and 5) the modified Tanford-Kirkwood theory over-screens the measured electrostatic interactions in subtilisin.

Binding Sites↗
PubMed1988

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis.

In this report we describe an accurate numerical method for calculating the total electrostatic energy of molecules of arbitrary shape and charge distribution, accounting for both Coulombic and solvent polarization terms. In addition to the solvation energies of individual molecules, the method can be used to calculate the electrostatic energy associated with conformational changes in proteins as well as changes in solvation energy that accompany the binding of charged substrates. The validity of the method is examined by calculating the hydration energies of acetate, methyl ammonium, ammonium, and methanol. The method is then used to study the relationship between the depth of a charge within a protein and its interaction with the solvent. Calculations of the relative electrostatic energies of crystal and misfolded conformations of Themiste dyscritum hemerythrin and the VL domain of an antibody are also presented. The results indicate that electrostatic charge-solvent interactions strongly favor the crystal structures. More generally, it is found that charge-solvent interactions, which are frequently neglected in protein structure analysis, can make large contributions to the total energy of a macromolecular system.

Binding, Competitive↗
PubMed1985

On the calculation of electrostatic interactions in proteins.

In this paper we present a classical treatment of electrostatic interactions in proteins. The protein is treated as a region of low dielectric constant with spherical charges embedded within it, surrounded by an aqueous solvent of high dielectric constant, which may contain a simple electrolyte. The complete analysis includes the effects of solvent screening, polarization forces, and self energies, which are related to solvation energies. Formulae, and sample calculations of forces and energies, are given for the special case of a spherical protein. Our analysis and model calculations point out that any consistent treatment of electrostatic interactions in proteins should account for the following. Solvent polarization is an important factor in the calculation of pairwise electrostatic interactions. Solvent polarization substantially affects both electrostatic energies and forces acting upon charges. No simple expression for the effective dielectric constant, Deff, can generally be valid, since Deff is a sensitive function of position. Solvent screening of pairwise interactions involving dipolar groups is less effective than the screening of charges. In fact for many interactions involving dipoles, solvent screening can be essentially ignored. The self energy of charges makes a large contribution to the total electrostatic energy of a protein. This must be compensated by specific interactions with other groups in the protein. Strategies for applying our analysis to proteins whose structures are known are discussed.

Electricity↗
PubMedDate not supplied

The binding database: overview and user's guide.

The large and growing body of experimental data on molecular binding is of enormous value in biology, pharmacology, and chemistry. Applications include the assignment of function to biomolecules, drug discovery, molecular modeling, and nanotechnology. However, binding data are difficult to find and access because they are available almost exclusively through scientific journals. BindingDB, a public, web-accessible database of measured binding affinities, is designed to address this problem. BindingDB collects data for natural and modified biomolecules and for synthetic compounds, and provides detailed experimental information. Currently, measurements by isothermal titration calorimetry are fully supported; measurements by enzyme inhibition will soon be included as well. The web site allows data to be searched by a range of criteria, including binding thermodynamics, sequence homology, and chemical structure, substructure, and similarity. Experimentalists are encouraged to publicize their data by entering it into BindingDB via the online forms. Such data can be updated or revised by the depositor, if necessary, and will remain publicly accessible. User involvement and feedback are welcomed.

Databases as Topic↗
PubMedDate not supplied

Calculation of electrostatic potentials in an enzyme active site.

To be able to calculate the contributions of individual amino acids to the electrostatic field of a protein would be of considerable value in designing proteins of enhanced or altered function and stability. Recent studies on the serine protease subtilisin provide direct measurements of the electrostatic potential in the active site of the enzyme produced by two charged amino acids. We have used these results to test a recently developed method for the calculation of electrostatic interactions between two specific sites on a protein. The extent of agreement between the theoretical and experimental results suggests that the continuum solvent model used in the calculations reproduces the essential features of the interaction.

Binding Sites↗