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H J Berendsen

Publications and source records attributed to H J Berendsen.

At least 19 recordsLinked to original sources
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↗
PubMed1992

Conformational search by potential energy annealing: algorithm and application to cyclosporin A.

A major problem in modelling (biological) macromolecules is the search for low-energy conformations. The complexity of a conformational search problem increases exponentially with the number of degrees of freedom which means that a systematic search can only be performed for very small structures. Here we introduce a new method (PEACS) which has a far better performance than conventional search methods. To show the advantages of PEACS we applied it to the refinement of Cyclosporin A and compared the results with normal molecular dynamics (MD) refinement. The structures obtained with PEACS were lower in energy and agreed with the NMR parameters much better than those obtained with MD. From the results it is further clear that PEACS samples a much larger part of the available conformational space than MD does.

Algorithms↗
PubMed1991

Conformational flexibility of aqueous monomeric and dimeric insulin: a molecular dynamics study.

A series of molecular dynamics simulations have been used to investigate the nature of monomeric and dimeric insulin in aqueous solution. It is shown that in the absence of crystal contacts both monomeric and dimeric insulin have a high degree of intrinsic flexibility. Neither of the two monomer conformations of 2Zn crystalline insulin appears to be favored in solution nor is the asymmetry of the crystal dimer reduced in the absence of crystal contacts. A shift is observed in the relative positions of molecules 1 and 2 in the dimer compared with that found in the crystal, which may have consequences for the prediction of the effects of mutants in the monomer-monomer interface designed to alter the self-association properties of insulin.

Amino Acid Sequence↗
PubMed1991

Stabilization of the neutral protease of Bacillus stearothermophilus by removal of a buried water molecule.

Using site-directed mutagenesis, Ala166 in the neutral protease of Bacillus stearothermophilus was changed into Ser. Model building and molecular dynamics simulations of the mutant enzyme indicated that the Ser hydroxyl group fits well in a cavity which contains a water molecule in the wild-type enzyme. The Ala166----Ser mutation was expected to exert a stabilizing effect because of the gain in entropy resulting from the release of water molecule from the folded protein to the solvent. In addition, the hydrogen-bonding network around residue 166 was improved upon the mutation. As a result of this mutation the thermostability of the neutral protease was increased by 1.2 +/- 0.1 degrees C.

Alanine↗
PubMed1991

Thermostability of Bacillus subtilis neutral protease.

The thermostability of the B. subtilis neutral protease was studied under various conditions. At elevated temperatures the enzyme was inactivated as a result of autolysis. The rate of inactivation did not depend on the enzyme concentration and the enzyme was most stable near its pH optimum. The rate of inactivation was unaffected by the presence of a second protease during the incubation at high temperatures. The results indicate that the rate of thermal inactivation of the neutral protease is determined by the kinetics of local unfolding processes that precede autolysis rather than by the catalytic rate of the autodigestion reaction or an irreversible unfolding step.

Bacillus subtilis↗
PubMed1991

On deriving spatial protein structure from NMR or X-ray diffraction data.

During the last decade it has become possible to derive the spatial structure of small proteins in solution using multidimensional NMR spectroscopy measurements and interpreting the data in terms of a chemical atomic model. The NMR experiments generate a set of interproton distance constraints, which is subsequently used to generate spatial structures that satisfy the experimental data. Correspondingly, crystallographic least-squares and molecular dynamics refinement is routinely applied to obtain a protein structure that is compatible with the observed structure factor amplitudes. The quality of the structure obtained will depend on the number and quality of the experimental data and on the searching power of the refinement method and protocol. The potential energy annealing conformational search (PEACS) algorithm is shown to be an improvement over standard molecular dynamics search methods. The use of time-dependent distance or structure factor restraints in molecular dynamics refinement yields a much better representation of experimental information than the fixed, static restraints which have generally been used until now. Conventional structure refinement methods lead to a too static and rigid picture of a protein in solution or in the crystalline state.

Algorithms↗
PubMed1990

Tertiary structure of two-electron reduced Megasphaera elsdenii flavodoxin and some implications, as determined by two-dimensional 1H-NMR and restrained molecular dynamics.

The tertiary structure of the non-crystallizable two-electron-reduced Megasphaera elsdenii flavodoxin (15 kDa, 137 amino acid residues) has been determined using nuclear Overhauser enhancement restraints extracted from two-dimensional 1H-NMR spectra. A tertiary structure satisfying the experimental restraints very well (maximum NOE violation of 66 pm) was obtained with use of restrained molecular dynamics, using 509 distance restraints (including one non-NOE) on a starting structure modeled from the crystal structure of one-electron-reduced Clostridium MP flavodoxin. The protein consists of a central parallel beta-sheet surrounded on both sides by two alpha-helices. The flavin is positioned at the periphery of the molecule. The tertiary structure of the protein is highly defined with the exception of the flavin. The latter is expected to result from performing the restrained molecular dynamics simulation without water molecules and without proper charges on the flavin. The flavin, including the phosphate, the ribityl side chain and the isoalloxazine ring, is solvent accessible under the experimental conditions used and evidenced by a two-dimensional amide exchange experiment. This accessibility is expected to be important in the redox potential regulation of the semiquinone/hydroquinone couple of the protein. The amide exchange against deuterons and several typical line shapes in the two-dimensional NMR spectra are consistent with the structure generated. The structure is discussed in detail.

Bacterial Proteins↗
PubMed1990

Proton-nuclear magnetic resonance relaxation times in brain edema.

Proton relaxation times of protein solutions, bovine brain, and edematous feline brain tissue were studied as a function of water concentration, protein concentration, and temperature. In accordance with the fast proton exchange model for relaxation, a linear relation could be established between R1 and the inverse of the weight fraction of tissue water. This relation also applied to R2 of gray matter and of protein solutions. No straightforward relation with water content was found for R2 of white matter. Temperature-dependent studies indicated that in this case, the slow exchange model for relaxation had to be applied. The effect of macromolecules in physiological relevant concentrations on the total relaxation behavior of edematous tissue was weak. Total water content changes predominantly affected the relaxation rates. The linear relation may have high clinical potential for assessment of the status of cerebral edema on the basis of T1 and T2 readings from MR images.

Animals↗
PubMed1989

Dynamical structure of carboxypeptidase A.

Structural fluctuations of the apoenzyme form of carboxypeptidase A (EC 3.4.12.2) have been evaluated on the basis of molecular dynamics. The Konnert-Hendrickson refined coordinates of 2437 non-hydrogen atoms of the 307 amino acid residues derived from the X-ray structure of the holoenzyme served as the molecular model together with 548 calculated polar hydrogen atoms and 25 buried solvent molecules. Molecular dynamics simulations were carried out at 277 K, and the averaged structural properties of the protein were evaluated for the terminal 20 picosecond portion of a 48 picosecond trajectory. The average atomic displacement from the initial X-ray structure was 2.49 A for all atoms and 1.79 A for C alpha atoms. The average root-mean-square (r.m.s.) fluctuation of all atoms was 0.67 A as compared to 0.54 A evaluated from the X-ray-defined temperature factors. Corresponding r.m.s. fluctuations for backbone atoms were 0.56 A by molecular dynamics and 0.49 A by X-ray. On the basis of these molecular dynamics studies of the isolated molecule, it is shown that amino acid residues corresponding to intermolecular contact sites of the crystalline enzyme are associated with high amplitude motion. All eight segments of alpha-helix and eight regions of beta-strand were well preserved except for unwinding of the five C-terminal residues of the alpha-helix 112-122 that form part of an intermolecular contact in the crystal. Four regions of beta-strand and one alpha-helix with residues adjacent to or in the active site constitute a core of constant secondary structure and are shown not to change in relative orientation to each other during the course of the trajectory. The absence of the zinc ion does not markedly influence the stereochemical relationships of active site residues in the dynamically averaged protein. The extent of motional fluctuations of each of the subsites of substrate recognition in the active site has been evaluated. Active site residues responsible for specificity of substrate binding or splitting of the scissile bond exhibit low simulated motion. In contrast, residues in more distal sites of substrate recognition exhibit markedly greater motional fluctuations. This differential extent of dynamical motion is related to structural requirements of substrate hydrolysis.

Amino Acid Sequence↗
PubMed1989

Unified multiple-feature color display for MR images.

A display method is proposed in which the spin-lattice relaxation time T1, the spin-spin relaxation time T2, and the proton density rho of each pixel in a MR image are simultaneously expressed in color features in a unified way that allows international standardization. MR images were made from a phantom, a healthy volunteer, and patients in such a way that T1 and T2 and proton density images could be derived. T1 and T2 data were compared with accurate relaxation time measurements of the phantom content. Color images were computed from the acquired T1 and T2 images using matrix multiplication on a pixel base. In this way the color combination in each pixel represents the properties of that particular pixel by a unique mixing of the elementary colors red, green, and blue. Color resolution could be modified using different choices of the reference triangle in which the color combinations were defined. This method of representation offers a means for displaying multiple features as T1 and T2 in one directly interpretable image, independent of instrumental settings.

Brain↗
PubMed1989

An NMR-based molecular dynamics simulation of the interaction of the lac repressor headpiece and its operator in aqueous solution.

The results of a 125 psec molecular dynamics simulation of a lac headpiece-operator complex in aqueous solution are reported. The complex satisfies essentially all experimental distance information derived from two-dimensional nuclear magnetic resonance (2-D-NMR) studies. The interaction between lac repressor headpiece and its operator is based on many direct- and water-mediated hydrogen bonds and nonpolar contacts which allow the formation of a tight complex. No stable hydrogen bonds between side chains and bases are found, while specific contacts occur between both nonpolar groups and, to a lesser extent, through water-mediated hydrogen bonds. The simulated complex structure in water is intrinsically stable without application of nuclear Overhauser effect (NOE) distance restraints, while being compatible with most of the available biochemical, genetic, and chemically induced dynamic nuclear polarization (CIDNP) data.

Binding Sites↗
PubMed1988

Nuclear magnetic resonance relaxation in experimental brain edema: effects of water concentration, protein concentration, and temperature.

Proton relaxation times T1 and T2 of macromolecular solutions, bovine brain tissues, and experimental cat brain edema tissues were studied as a function of water concentration, protein concentration, and temperature. A linear relation was found between the inverse of the weight fraction of tissue water and the spin-lattice relaxation rate, R1, based on a fast proton exchange model for relaxation. This correlation was also found for the spin-spin relaxation rate, R2, of gray matter samples and macromolecular solutions at low concentrations. Concentrated solutions of protein-water samples showed an enhanced relaxation due to viscosity effects. The T2 of white matter was considerably lengthened with elevated water concentration, but showed no straightforward relation with the total tissue water content. The relaxation times of all samples increased with temperature, supporting the assumption of fast proton exchange in the model for relaxation. This was not found for white matter, in which T2 decreased with increasing temperature, which indicated that intermediate or even slow exchange was present. The relation found between relaxation times and tissue water content can be used to predict the amount of and/or increase in tissue water due to water-elevating processes such as edema.

Animals↗
PubMed1988

Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: application to the DNA binding domain of lac repressor from Escherichia coli.

The technique of two-dimensional nuclear magnetic resonance (2D-NMR) has recently assumed an active role in obtaining information on structures of polypeptides, small proteins, sugars, and DNA fragments in solution. In order to generate spatial structures from the atom-atom distance information obtained by the NMR method, different procedures have been developed. Here we introduce a combined procedure of distance geometry (DG) and molecular dynamics (MD) calculations for generating 3D structures that are consistent with the NMR data set and have reasonable internal energies. We report the application of the combined procedure on the lac repressor DNA binding domain (headpiece) using a set of 169 NOE and 17 "hydrogen bond" distance constraints. Eight of ten structures generated by the distance geometry algorithm were refined within 10 ps MD simulation time to structures with low internal energies that satisfied the distance constraints. Although the combination of DG and MD was designed to combine the good sampling properties of the DG algorithm with an efficient method of lowering the internal energy of the molecule, we found that the MD algorithm contributes significantly to the sampling as well.

Algorithms↗
PubMed1987

Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry.

A new and promising development in the field of computer simulation of molecular systems is the so-called thermodynamic cycle integration technique, which combines well-known results from statistical thermodynamics with powerful computer simulation methods. The basic formulas, the development and the applications in the areas of drug design, protein engineering and conformational analysis of this elegant technique are discussed.

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↗
PubMed1987

Interpretation of magnetic resonance images making use of in vitro examinations of spinal tissue.

T1 and T2 relaxation times were determined in vitro at 21 MHz (0.5 T) for a variety of spinal and paraspinal tissues. Intensity formulas for spin echo and inversion recovery sequences were derived and used to calculate the intensities of these tissues as they would appear in magnetic resonance images. The intensity was calculated as a function of various repetition, echo, and inversion times. It is shown that the combination of acquiring in vitro relaxation time values and calculating intensity as a function of pulse timings is useful to predict the parameter setting for optimal contrast between certain tissues without applying series of magnetic resonance images.

Electron Spin Resonance Spectroscopy↗
PubMed1986

Simulations of proteins in water.

Molecular dynamics simulations of hydrated protein crystals have been carried out in only three cases: two simulations of pancreatic trypsin inhibitor (PTI) and one of avian pancreatic polypeptide (aPP). The purpose of such simulations is to evaluate the accuracy and reliability of molecular dynamics simulations of hydrated proteins. A 40-psec simulation on crystalline PTI, involving 4 protein molecules (of 58 amino acids each), 552 water molecules, and 24 Cl- ions is described. Considerations are energetic and structural stability, division of interaction energy among water and protein, and precision of average structure and structural fluctuations compared to X-ray data from a new 0.94-A resolution study of Wlodawer et al. Water and ion dynamics are considered by analysis of diffusional motions and of residence times of water molecules in specific sites.

Computer Simulation↗