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M Karplus

Publications and source records attributed to M Karplus.

At least 181 records · Page 10Linked to original sources
PubMed1989

Construction of side-chains in homology modelling. Application to the C-terminal lobe of rhizopuspepsin.

A detailed and rule-based side-chain modelling procedure for globular proteins is presented. It uses the conformational information contained in a homologous (template) structure as a starting point and includes recipes for atom placement and for checking and improving the atomic positions. The scheme does not rely on intuitive judgements or visual examination of the model during construction or refinement. It comprises four stages; the first three are relatively simple and the fourth is more complex. In the first stage, initial conformations for as many atoms as possible are transferred from the template structure based on the application of trends reported previously. Second, these trends are used to correct poor van der Waals overlaps. Third, the remaining side-chains atoms (those for which no information is contained in the template) are placed by evaluating their rigid rotation, van der Waals surfaces. The fourth stage consists of a hierarchial series of conformational checks. They involve the evaluation of individual residue energies in the absence and presence of the rest of the protein relative to statistical trends observed in the template structure, the comparison of hydrogen-bonding patterns and side-chain accessibilities in the model and template and brief energy minimization followed by an evaluation of the rigid rotation potential energy surfaces of each side-chain. The checks pinpoint "incorrectly" modelled side-chains, suggest conformational changes and provide a means for determining the portions of the model that are likely to be correct and those likely to be in error. The procedure developed in the paper is tested by modelling the side-chains of the C-terminal lobe of the aspartyl proteinase rhizopuspepsin, using the rhizopuspepsin backbone and the homologous protein, penicillopepsin, as a template for the side-chains. The resultant model was compared to the high-resolution X-ray structure of rhizopuspepsin. Using penicillopepsin data only (stage I), 58% of the chi 1 dihedrals and 44% of the chi 2 dihedrals were modelled correctly. Once poor van der Waals overlaps had been corrected and all of the atoms had been placed (stages II and III), 86% of the chi 1 dihedrals and 75% of the chi 2 dihedrals were correct. After the refinement had been completed (stage IV), 92% of the chi 1 dihedrals and 81% of the chi 2 dihedrals were correctly positioned.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1989

Two-dimensional NMR and photo-CIDNP studies of the insulin monomer: assignment of aromatic resonances with application to protein folding, structure, and dynamics.

The aromatic 1H NMR resonances of the insulin monomer are assigned at 500 MHz by comparative studies of chemically modified and genetically altered variants, including a mutant insulin (PheB25----Leu) associated with diabetes mellitus. The two histidines, three phenylalanines, and four tyrosines are observed to be in distinct local environments; their assignment provides sensitive markers for studies of tertiary structure, protein dynamics, and protein folding. The environments of the tyrosine residues have also been investigated by photochemically induced dynamic nuclear polarization (photo-CIDNP) and analyzed in relation to packing constraints in the crystal structures of insulin. Dimerization involving specific B-chain interactions is observed with increasing protein concentration and is shown to depend on temperature, pH, and solvent composition. In the monomer large variations are observed in the line widths of amide resonances, suggesting intermediate exchange among conformational substates; such substates may relate to conformational changes observed in different crystal states and proposed to occur in the hormone-receptor complex. Additional evidence for multiple conformations in solution is provided by comparative studies of an insulin analogue containing a peptide bond between residues B29 and A1 (mini-proinsulin). This analogue forms dimers and higher-order oligomers under conditions in which native insulin is monomeric, suggesting that the B29-A1 peptide bond stabilizes a conformational substate favorable for dimerization. Such stabilization is not observed in corresponding studies of native proinsulin, in which a 35-residue connecting peptide joins residues B30 and A1; this extended tether is presumably too flexible to constrain the conformation of the B-chain. The differences between proinsulin and mini-proinsulin suggest a structural mechanism for the observation that the fully reduced B29-A1 analogue folds more efficiently than proinsulin to form the correct pattern of disulfide bonds. These results are discussed in relation to molecular mechanics calculations of insulin based on the available crystal structures.

Circular Dichroism↗
PubMed1989

Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme.

The stochastic boundary molecular dynamics methodology is applied to the active site of the enzyme lysozyme. A comparison is made of in vacuo dynamics results from the stochastic boundary method and a full conventional molecular dynamics simulation of lysozyme. Excellent agreement between the two approaches is obtained. The influence of solvent on the residues in the active site region is explored and it is shown that both the structure and dynamics are affected. Of particular importance for the structure of the protein is the solvation of polar residues and the stabilization of like-charged ion pairs. The magnitude of the fluctuations is only slightly altered by the solvent; the overall increase in the root-mean-square fluctuations, relative to the vacuum run, is 11%. The solvent effect on dynamical properties is found not to be simply related to the solvent viscosity. Both the solvent exposure and dynamic aspects of protein-solvent interactions, including the relative time scales of the motions, are shown to play a role. The effects of the protein on solvent dynamics and structure are also observed to be significant. The solvent molecules around atoms in charged, polar and apolar side-chains show markedly different diffusion coefficients as well as exhibiting different solvation structures. One key example is the water around apolar groups, which is much less mobile than bulk water, or water solvating polar groups.

Animals↗
PubMed1989

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis.

A molecular dynamics simulation method is used to determine the contributions of individual amino acid residues and solvent molecules to free energy changes in proteins. Its application to the hemoglobin interface mutant Asp G1(99) beta----Ala shows that some of the contributions to the difference in the free energy of cooperativity are as large as 60 kilocalories (kcal) per mole. Since the overall free energy change is only -5.5 kcal/mole (versus the experimental value of -3.4 kcal/mole), essential elements of the thermodynamics are hidden in the measured results. By exposing the individual contributions, the free energy simulation provides new insights into the origin of thermodynamic changes in mutant proteins and demonstrates the role of effects beyond those usually considered in structural analyses.

Alanine↗
PubMed1989

X-ray refinement of protein structures by simulated annealing: test of the method on myohemerythrin.

The recently developed method of structure factor refinement by molecular dynamics with simulated annealing [Brünger, Kuriyan & Karplus (1987). Science, 235, 458-460] is tested on the 118 residue protein myohemerythrin. A highly refined structure for this protein at 1.3/1.7 A resolution has recently been published [Sheriff, Hendrickson & Smith (1987). J. Mol. Biol. 197, 273-296]. This is compared with the results of simulated annealing refinement (with no manual intervention) starting from an earlier model for the protein from a stage in the refinement when conventional least-squares methods could not improve the structure. Simulated annealing reduces the R factor at 2.5 A from 39 to 31%, with uniform temperature factors and no solvent molecules and with similar stereochemistry; the comparable value for the manually refined structure is 27.9%. Errors in backbone and sidechain positions up to about 3 A are corrected by the method. The error in backbone positions for roughly 85% of the initial structure is within this range, and in these regions the r.m.s. backbone error is reduced from 1.1 to 0.4 A. For the rest of the structure, including a region which was incorrectly built due to a sequence error, the procedure does not yield any improvement and manual intervention appears to be required. Nevertheless, the overall improvement in the structure results in electron density maps that are easier to interpret and permit identification of the errors in the structure. The general utility of the simulated annealing methodology in X-ray refinement is discussed.

Evaluation Studies as Topic↗
PubMed1989

A molecular dynamics analysis of protein structural elements.

The relation between protein secondary structure and internal motions was examined by using molecular dynamics to calculate positional fluctuations of individual helix, beta-sheet, and loop structural elements in free and substrate-bound hen egg-white lysozyme. The time development of the fluctuations revealed a general correspondence between structure and dynamics; the fluctuations of the helices and beta-sheets converged within the 101 psec period of the simulation and were lower than average in magnitude, while the fluctuations of the loop regions were not converged and were mostly larger than average in magnitude. Notable exceptions to this pattern occurred in the substrate-bound simulation. A loop region (residues 101-107) of the active site cleft had significantly reduced motion due to interactions with the substrate. Moreover, part of a loop and a 3(10) helix (residues of 67-88) not in contact with the substrate showed a marked increase in fluctuations. That these differences in dynamics of free and substrate-bound lysozyme did not result simply from sampling errors was established by an analysis of the variations in the fluctuations of the two halves of the 101 psec simulation of free lysozyme. Concerted transitions of four to five mainchain phi and psi angles between dihedral wells were shown to be responsible for large coordinate shifts in the loops. These transitions displaced six or fewer residues and took place either abruptly, in 1 psec or less, or with a diffusive character over 5-10 psec. Displacements of rigid secondary structures involved longer timescale motions in bound lysozyme; a 0.5 A rms change in the position of a helix occurred over the 55 psec simulation period. This helix reorientation within the protein appears to be a response to substrate binding. There was little correlation between the solvent accessible surface area and the dynamics of the different structural elements.

Binding Sites↗
PubMed1989

Protein secondary structure prediction with a neural network.

A method is presented for protein secondary structure prediction based on a neural network. A training phase was used to teach the network to recognize the relation between secondary structure and amino acid sequences on a sample set of 48 proteins of known structure. On a separate test set of 14 proteins of known structure, the method achieved a maximum overall predictive accuracy of 63% for three states: helix, sheet, and coil. A numerical measure of helix and sheet tendency for each residue was obtained from the calculations. When predictions were filtered to include only the strongest 31% of predictions, the predictive accuracy rose to 79%.

Amino Acids↗
PubMed1988

Electrostatic effects of charge perturbations introduced by metal oxidation in proteins. A theoretical analysis.

A macroscopic dielectric model for the interactions between charges in proteins is used to calculate the changes in His residue pKa values induced in azurin by oxidation of the copper. The calculated results agree with nuclear magnetic resonance experiments to within the uncertainty associated with the measurements. It is found that a large apparent dielectric constant can describe the interaction between two protein groups, even if the shortest path between them is through the protein, which is assumed to have a low dielectric constant.

Azurin↗
PubMed1988

Inelastic neutron scattering analysis of picosecond internal protein dynamics. Comparison of harmonic theory with experiment.

The experimental inelastic neutron scattering spectrum of a protein, the bovine pancreatic trypsin inhibitor (BPTI), in a powder sample is presented together with the generalized density of states, G(omega), as a function of the frequency, omega, derived from the scattering data. The experimental results are compared with calculations from two different normal mode analyses of BPTI. One of these, based on an improved model, gives a calculated spectrum and density of states in general agreement with those obtained experimentally; the other, based on an earlier model, shows considerable disagreement. The important improvements in the newer normal mode analysis are the explicit treatment of all atoms (non-polar as well as polar hydrogens are included) and a modified truncation scheme for the long-range electrostatic interactions. The fact that the inelastic neutron scattering measurements can distinguish between the two theoretical models makes clear their utility for the analysis of protein dynamics.

Animals↗
PubMed1988

Anisotropy and anharmonicity of atomic fluctuations in proteins: implications for X-ray analysis.

The effects of anisotropy and anharmonicity of the atomic fluctuations on the results of crystallographic refinement of proteins are examined. Atomic distribution functions from a molecular dynamics simulation for lysozyme are introduced into a real-space (electron density) refinement procedure for individual atoms. Several models for the atomic probability distributions are examined. When isotropic, harmonic motion is assumed, the largest discrepancies between the true first moments (means) and second moments (B factors) of the positions calculated from the dynamics and the fitted values occur for probability densities with multiple peaks. The refined mean is at the center of the largest peak, and the refined B factor is slightly larger than that of the largest peak, unless the distance between the peaks is small compared to the peak width. The resulting values are often significantly different from the true first and second moments of the distribution. To improve the results, alternate conformations, rather than anharmonic corrections, should be included.

Mathematics↗
PubMed1988

Analysis of proton release in oxygen binding by hemoglobin: implications for the cooperative mechanism.

The relationship in hemoglobin between cooperativity (dependence of the Hill constant on pH0 and the Bohr effect (dependence of the mean oxygen affinity on pH) can be described by a statistical thermodynamic model [Szabo, A., & Karplus, M. (1972) J. Mol. Biol. 72, 163-197; Lee, A., & Karplus, M. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 7055-759]. In this model, salt bridges and other interactions serve to couple tertiary and quaternary structural changes. To test and refine the model, it is applied to the analysis of the pH dependence of the tetramer Adair constants corrected for statistical factors (K4i', i = 1-4). Attention is focused on the proton release of the first (delta H1+ = alpha log K41'/alpha pH) and last (delta H4+ = alpha log K44'/alpha pH) oxygenation steps, where K4i' are the Adair constants corrected for statistical factors. Measurements of delta H1+ and delta H4+ under carefully controlled conditions are reported, and good agreement between the model calculation and these experimental results is obtained. The salt bridges are found to be partially coupled to the ligation state in the deoxy quaternary structure; it is shown that a Monod-Wyman-Changeux-type model, in which the salt bridges are coupled only to quaternary structural change, is inconsistent with the data for delta H1. The significance of the present analysis for an evaluation of the Perutz mechanism [Perutz, M.F. (1970) Nature (London) 228, 726-734, 734-739] and other models for hemoglobin cooperativity is discussed.

Humans↗
PubMed1988

Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison.

A method for the prediction of hydrogen positions in proteins is presented. The method is based on the knowledge of the heavy atom positions obtained, for instance, from X-ray crystallography. It employs an energy minimization limited to the environment of the hydrogen atoms bound to a common heavy atom or to a single water molecule. The method is not restricted to proteins and can be applied without modification to nonpolar hydrogens and to nucleic acids. The method has been applied to the neutron diffraction structures of trypsin, ribonuclease A, and bovine pancreatic trypsin inhibitor. A comparison of the constructed and the observed hydrogen positions shows few deviations except in situations in which several energetically similar conformations are possible. Analysis of the potential energy of rotation of Lys amino and Ser, Thr, Tyr hydroxyl groups reveals that the conformations of lowest intrinsic torsion energies are statistically favored in both the crystal and the constructed structures.

Hydrogen↗
PubMed1988

Diffusion-collision model for the folding kinetics of myoglobin.

The diffusion-collision model has been used to analyze the folding kinetics of myoglobin. The microdomains, which are the basic units that coalesce during the folding, are identified with the helices and the stabilizing contacts between helices are determined from the native structure. Both association and dissociation reactions are included and a range of stabilization parameters is investigated to determine the variation in overall rate and the relative contributions made by different intermediates during the folding process. In a comparison of folding to the native state and to the midpoint of the folding transition (i.e., 50% native protein at the completion of the reaction) significant differences in the contributing intermediates are found.

Diffusion↗
PubMed1988

The effects of brain bilirubin deposition on auditory brain stem evoked responses in rats.

Auditory brain stem evoked responses (ABR) in newborn infants are altered by elevated serum bilirubin levels and may be used as an indicator of bilirubin toxicity. The hypothesis of our study was that hyperbilirubinemia may affect ABR's because of bilirubin deposition in the brain stem. We examined this hypothesis by studying 21 male adult rats divided into three groups: group A, control (n = 8); group B, low bilirubin (n = 6); and group C, high bilirubin (n = 7). Each experimental group was studied over 150 min. The control group received a buffer solution. The low bilirubin group received a low dose bilirubin bolus of 50 mg/kg followed by continuous infusion of 20 mg/kg/h. The high bilirubin group received a bolus of 100 mg/kg bilirubin followed by continuous infusion of 40 mg/kg/h. All groups received sulfisoxazole (50 mg/kg X 3) during the second hour of the study. Auditory evoked potentials were recorded at 0 and 150 min. At the end of the study, the brains were analyzed for bilirubin content. Bilirubin deposition in the 3 groups was 0.6 +/- 0.28 micrograms/g, 0.93 +/- 0.07 micrograms/g and 3.2 +/- 2.2 micrograms/g for the control, low bilirubin and high bilirubin groups, respectively. Bilirubin deposition in the brain was associated with a significant amplitude reduction of Wave I and III, but had no effect on absolute latencies and interpeak latencies. Very high brain bilirubin concentrations were associated with absence of Waves I and IV. Wave I was also significantly reduced in the low bilirubin group where there was slightly increased bilirubin deposition in the brain. We conclude that ABR changes in the form of wave amplitude reduction were associated with brain stem and cerebellum bilirubin deposition. We speculate that previously reported observations of abnormal ABR changes in hyperbilirubinemic newborn infants are associated with bilirubin deposition.

Animals↗
PubMed1988

The normal modes of the gramicidin-A dimer channel.

The dynamics of the gramicidin-A dimer channel is studied in the harmonic approximation by a vibrational analysis of the atomic motions relative to their equilibrium positions. The system is represented by an empirical potential energy function, and all degrees of freedom (bonds lengths, bond angles, and torsional angles) are allowed to vary. The thermal fluctuations in the backbone dihedral angles phi and psi, atomic root mean square displacements, and the correlations between the different amide planes are computed. It is found that only adjacent dihedral psi i and phi i+1 are strongly correlated, while different hydrogen-bonded amide planes are only weakly correlated. Modes with relatively low vibrational frequencies (75-175 cm-1) make the dominant contributions to the carbonyl librations. The general flexibility of the structure and the role of carbonyl librations in the ion transport mechanism are discussed.

Biophysical Phenomena↗
PubMed1987

Electrostatic effects and hydrogen exchange behaviour in proteins. The pH dependence of exchange rates in lysozyme.

The pH dependence of the exchange rates for a number of tryptophan and amide hydrogen atoms in hen egg-white lysozyme has been determined at temperatures well below the thermal denaturation temperature. The pH behaviour of each hydrogen is unique and can differ markedly from that of simple compounds. A model for electrostatic effects in proteins is described and used to explain a number of the features of the pH dependence of the exchange rates of certain hydrogens. The results indicate that exchange takes place from a conformation of the protein closely similar to that of the native protein, with local fluctuations providing the mechanism for exchange. For the more-buried hydrogens at low pH values there is a general increase in the exchange rates caused by the decreasing stability of the protein as calculated from the electrostatic model. The analysis shows how evidence from hydrogen exchange studies can be used to provide information about electrostatic interactions in localized regions of proteins. A description of the electrostatic model and some applications are given in the Appendix.

Amino Acid Sequence↗
PubMed1987

Trypsinogen-trypsin transition: a molecular dynamics study of induced conformational change in the activation domain.

The trypsinogen to trypsin transition has been investigated by a stochastic boundary molecular dynamics simulation that included a major portion of the trypsin molecule and the surrounding solvent. Attention focused on the "activation domain", which crystallographic studies have shown to be ordered in trypsin and disordered in its zymogen, trypsinogen. The chain segments that form the activation domain were found to exhibit large fluctuations during the simulation of trypsin. To model a difference between trypsin and trypsinogen, the N-terminal residues Ile-16 and Val-17 were removed in the former and replaced by water molecules. As a result of the perturbation, a structural drift of 1-2 A occurred that is limited to the activation domain. Glycine residues are found to act as hinges for the displaced chain segments.

Amino Acid Sequence↗