Biomedical subjects

A P Heiner

Publications and source records attributed to A P Heiner.

3 recordsLinked to original sources

PubMed1993

Structure prediction of subtilisin BPN' mutants using molecular dynamics methods.

In this paper we describe the achievements and pitfalls encountered in doing structure predictions of protein mutants using molecular dynamics simulation techniques in which properties of atoms are slowly changed as a function of time. Basically the method consists of a thermodynamic integration (slow growth) calculation used for free energy determination, but aimed at structure prediction; this allows for a fast determination of the mutant structure. We compared the calculated structure of the mutants Met222Ala, Met222Phe and Met222Gln of subtilisin BPN' with the respective X-ray structures and found good agreement between predicted and X-ray structure. The conformation of the residue subject to the mutation is relatively easy to predict and is mainly determined by packing criteria. When the side chain has polar groups its exact orientation may pose problems; long-range Coulomb interactions may generate a polarization feedback involving system relaxation times beyond the simulation time. Changes induced in the environment are harder to predict using this method. In particular, rearrangement of the hydration structure was difficult to predict correctly, probably because of the long relaxation times. In all conversions made the changes observed in the environment were found to be history-dependent and in particular the hydrogen bonding patterns provided evidence for metastable substates. In all cases the structure predicted was compared with available kinetic data and the reduced activity could be explained in terms of changes in the configuration of the active site.

Binding Sites↗

PubMed1992

MD simulation of subtilisin BPN' in a crystal environment.

In this paper we present a molecular dynamics (MD) simulation of subtilisin BPN' in a crystalline environment containing four protein molecules and solvent. Conformational and dynamic properties of the molecules are compared with each other and with respect to the X-ray structure to test the validity of the force field. The agreement between simulated and experimental structure using the GROMOS force field is better than that obtained in the literature using other force fields for protein crystals. The overall shape of the molecule is well preserved, as is the conformation of alpha-helices and beta-strands. Structural differences are mainly found in loop regions. Solvent networks found in the X-ray structure were reproduced by the simulation, which was unbiased with respect to the crystalline hydration structure. These networks seem to play an important role in the stability of the protein; evidence of this is found in the structure of the active site. The weak ion binding site in the X-ray structure of subtilisin BPN' is occupied by a monovalent ion. When a calcium ion is placed in the initial structure, three peptide ligands are replaced by 5 water ligands, whereas a potassium ion retains (in part) its original ligands. Existing force fields yield a reliable method to probe local structure and short-time dynamics of proteins, providing an accuracy of about 0.1 nm.

Computer Simulation↗

PubMed1987

Multi-exponential relaxation analysis with MR imaging and NMR spectroscopy using fat-water systems.

This study was undertaken to evaluate the feasibility of multiexponential relaxation data analysis to MR imaging techniques. The first part of this study contains accurate relaxation time measurements performed on a conventional spectrometer. In the second part, essentially the same measuring techniques were applied but now on standard whole body MR imaging equipment. T2 relaxation was measured using multi-echo techniques, T1 relaxation using multiple inversion recovery measurements. Manganese chloride solutions were used for verification of the single exponential model. Water and fat mixtures were considered for multi-exponentiality. Pure fat showed an intrinsic two-exponentiality in T1 and T2 relaxation. Mixtures of fat and water were analyzed and could at best be characterized by two exponentials, although at least three exponentials were known to be present. From the two-exponential fit the relative amounts of fat and water were calculated and compared with the mixture composition. Statistical criteria are discussed to discriminate between single and double exponential behavior in relaxation curves. It is concluded that the time consuming IR measurements for the determination of multiple T1 relaxation are not applicable in a clinical environment. Multiple T2 relaxation can be determined in a reasonable amount of time using multiple echo measurements in one image acquisition. It is shown that the observed values of T1 and T2 from tissues with intrinsic multiexponential relaxation behavior, measured with MR imaging or MR relaxation techniques on a whole-body imager or a conventional spectrometer, depend strongly on the way the experiments are set up and on the model accepted for data analysis.

Fats↗