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M Karplus

Publications and source records attributed to M Karplus.

At least 109 records · Page 6Linked to original sources
PubMed1995

Neural networks for secondary structure and structural class predictions.

A pair of neural network-based algorithms is presented for predicting the tertiary structural class and the secondary structure of proteins. Each algorithm realizes improvements in accuracy based on information provided by the other. Structural class prediction of proteins nonhomologous to any in the training set is improved significantly, from 62.3% to 73.9%, and secondary structure prediction accuracy improves slightly, from 62.26% to 62.64%. A number of aspects of neural network optimization and testing are examined. They include network overtraining and an output filter based on a rolling average. Secondary structure prediction results vary greatly depending on the particular proteins chosen for the training and test sets; consequently, an appropriate measure of accuracy reflects the more unbiased approach of "jackknife" cross-validation (testing each protein in the data-base individually).

Algorithms↗
PubMed1995

Zinc binding in proteins and solution: a simple but accurate nonbonded representation.

Force field parameters that use a combination of Lennard-Jones and electrostatic interactions are developed for divalent zinc and tested in solution and protein simulations. It is shown that the parameter set gives free energies of solution in good agreement with experiment. Molecular dynamics simulations of carboxypeptidase A and carbonic anhydrase are performed with these zinc parameters and the CHARMM 22 beta all-atom parameter set. The structural results are as accurate as those obtained in published simulations that use specifically bonded models for the zinc ion and the AMBER force field. The inclusion of longer-range electrostatic interactions by use of the Extended Electrostatics model is found to improve the equilibrium conformation of the active site It is concluded that the present parameter set, which permits different coordination geometries and ligand exchange for the zinc ion, can be employed effectively for both solution and protein simulations of zinc-containing systems.

Binding Sites↗
PubMed1995

Evaluation of comparative protein modeling by MODELLER.

We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by MODELLER, a program for comparative protein modeling by satisfaction of spatial restraints. The models have good stereochemistry and are at least as similar to the crystallographic structures as the closest template structures. The largest errors occur in the regions that were not aligned correctly or where the template structures are not similar to the correct structure. These regions correspond predominantly to exposed loops, insertions of any length, and non-conserved side chains. When a template structure with more than 40% sequence identity to the target protein is available, the model is likely to have about 90% of the mainchain atoms modeled with an rms deviation from the X-ray structure of approximately 1 A, in large part because the templates are likely to be that similar to the X-ray structure of the target. This rms deviation is comparable to the overall differences between refined NMR and X-ray crystallography structures of the same protein.

Amino Acid Sequence↗
PubMed1995

An automated method for dynamic ligand design.

An automated method for the dynamic ligand design (DLD) for a binding site of known structure is described. The method can be used for the creation of de novo ligands and for the modification of existing ligands. The binding site is saturated with atoms (sp3 carbon atoms in the present implementation) that form molecules under the influence of a potential function that joins atoms to each other with the correct stereochemistry. The resulting molecules are linked to precomputed functional group minimum energy positions in the binding site. The generalized potential function allows atoms to sample a continuous parameter space that includes the Cartesian coordinates and their occupancy and type, e.g., the method allows change of an sp3 carbon into an sp2 carbon or oxygen. A parameter space formulated in this way can then be sampled and optimized by a variety of methods. In this work, molecules are generated by use of a Monte Carlo simulated annealing algorithm. The DLD method is illustrated by its application to the binding site of FK506 binding protein (FKBP), an immunophilin. De novo ligands are designed and modification of the immunosuppressant drug FK506 are suggested. The results demonstrate that the dynamic ligand design approach can automatically construct ligands which complement both the shape and charge distribution of the binding site.

Algorithms↗
PubMed1995

Breech presentation and cesarean section in term nulliparous women.

OBJECTIVE: To examine pregnancy outcome in nulliparous women with single term breech presentation. METHODS: Two departments of Obstetrics and Gynecology at the same hospital used different approaches to deliver nulliparous women with singleton breech presentation at term. One department (A) delivered by trial of labor and the other (B) delivered by elective cesarean section. Prospectively and blinded to obstetric condition, parturients were assigned to either department in a systematic alternate fashion. The study period covered 8 years (1985-1992). The pregnancy outcome parameters examined were: Apgar score, intra- and post-partum death and maternal and neonatal morbidity. Neonatal morbidity was classified in three major categories: non-neurological trauma, neurological signs and respiratory problems. RESULTS: The study included 264 women of whom 135 delivered in department A and 129 in department B. Department A had 35 vaginal and 100 cesarean births and department B 10 vaginal and 119 cesarean births. There was no intra-partum death and the only post-partum death occurred among vaginal deliveries. The Apgar score was significantly worse at 1 and 5 min in vaginally delivered babies of department B. Neonatal morbidity was significantly more frequent after vaginal births (P < 0.01). Maternal morbidity was significantly higher following cesarean sections (P < 0.01). Babies of vaginal deliveries had significantly higher non-neurological trauma (P < 0.01) and pathological neurological signs (P < 0.01) than those delivered by the abdominal route. CONCLUSION: The level of risk for mother and child in the nulliparous with term singleton breech, suggests cesarean section as the preferred route of delivery.

Adult↗
PubMed1995

Theoretical studies of protein folding and unfolding.

The mechanism of protein folding is being investigated theoretically by the use of both simplified and all-atom models of the polypeptide chain. Lattice heteropolymer simulations of the folding process have led to proposals for the folding mechanism and for the resolution of the Levinthal paradox. Both stability and rapid folding have been shown in model studies to result from the presence of a pronounced global energy minimum corresponding to the native state. Concomitantly, molecular dynamics simulations with detailed atomic models have been used to analyze the initial stages of protein unfolding. Results concerning possible folding intermediates and the role of water in the unfolding process have been obtained. The two types of theoretical approaches are providing information essential for an understanding of the mechanism of protein folding and are useful for the design of experiments to study the mechanism in different proteins.

Models, Theoretical↗
PubMed1995

Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy.

The structural and thermodynamic factors responsible for the singly and doubly occupied saturation states of the gramicidin channel are investigated with molecular dynamics simulations and free energy perturbation methods. The relative free energy of binding of all of the five common cations Li+, Na+, K+, Rb+, and Cs+ is calculated in the singly and doubly occupied channel and in bulk water. The atomic system, which includes the gramicidin channel, a model membrane made of neutral Lennard-Jones particles and 190 explicit water molecules to form the bulk region, is similar to the one used in previous work to calculate the free energy profile of a Na+ ion along the axis of the channel. In all of the calculations, the ions are positioned in the main binding sites located near the entrances of the channel. The calculations reveal that the doubly occupied state is relatively more favorable for the larger ions. Thermodynamic decomposition is used to show that the origin of the trend observed in the calculations is due to the loss of favorable interactions between the ion and the single file water molecules inside the channel. Small ions are better solvated by the internal water molecules in the singly occupied state than in the doubly occupied state; bigger ions are solvated almost as well in both occupation states. Water-channel interactions play a role in the channel response. The observed trends are related to general thermodynamical properties of electrolyte solutions.

Binding Sites↗
PubMed1995

Use of a minimum perturbation approach to predict TIM mutant structures.

A minimum perturbation conformational search approach is used to model the structures of the yeast triosephosphate isomerase (TIM) single mutant in which the catalytic base Glu165 is changed to Asp, and the double mutant in which Glu165 is changed to Asp and Ser96 to Pro. In chicken TIM this double mutant is referred to as a pseudo-revertant because some of the catalytic activity lost due to the first mutation is regained when the second mutation occurs. Three minimum energy structures were calculated for the Asp165 conformation in the yeast TIM single mutant and another three for the double mutant. One of the calculated minimum energy conformations for Asp165 in the E165D structure agrees well with the X-ray structure. However, this conformation is not that of the lowest energy and is not one of the three most common conformers for Asp found by Ponder and Richards. This suggests that when an amino acid is introduced it may not be able to conform to the more general rules that apply to protein structures of evolutionary origin. While the van der Waals energy largely determines the allowed minima, the relative ranking of the final minima is determined by electrostatic effects and can therefore be affected by the inclusion of crystal waters in the calculation. When the E165D calculation is repeated with an active-site water molecule fixed in its E165D X-ray structure position, the relative ranking of the minima shifts and the X-ray conformation for Asp165 is the lowest interaction energy conformer. Two of the E165D calculated minimum energy structures are essentially identical to two of the S96P/E165D minima. All of the calculated minima for both the E165D and S96P/E165D mutants position the Asp side chain such that the anti-orbital, and not the more basic syn-orbital, of the carboxylate would be utilized for proton abstraction. This observation may explain why the chicken TIM S96P/E165D mutant, for which the X-ray structure indicates that the syn-orbital is used, is a pseudo-revertant while the yeast TIM double mutant is not; no X-ray structure is available for the latter. The multiplicity of minima found in the present analysis makes clear that predicting the exact orientation of a single side chain is not as simple as might be expected.

Amino Acid Sequence↗
PubMed1994

Analysis of two-residue turns in proteins.

The conformational properties of tight two-residue beta-turns in proteins are examined by empirical energy function calculations. Twenty-five tight turns are studied in isolation, in the presence of the protein, and in the presence of the protein and crystal water molecules. The conformational properties are subdivided into those that are intrinsic to the turn and those that depend on the protein and water environment. Two factors are shown to determine the conformation of a tight beta-turn. One is the twist of the beta-sheet (responsible for selecting either a type I' or II' conformation as opposed to the more common types I or II) and the other is a local electrostatic effect (responsible for distinguishing between the type I' and II' conformations). In the rare cases where a two-residue turn is found in a type I conformation, there exists a stabilizing feature (turn-protein interaction, a side-chain in a conformation that stabilizes type I, etc.) which compensates for the unfavorable twist of the turn relative to the beta-sheet.

Amino Acids↗
PubMed1994

How does a protein fold?

The number of all possible conformations of a polypeptide chain is too large to be sampled exhaustively. Nevertheless, protein sequences do fold into unique native states in seconds (the Levinthal paradox). To determine how the Levinthal paradox is resolved, we use a lattice Monte Carlo model in which the global minimum (native state) is known. The necessary and sufficient condition for folding in this model is that the native state be a pronounced global minimum on the potential surface. This guarantees thermodynamic stability of the native state at a temperature where the chain does not get trapped in local minima. Folding starts by a rapid collapse from a random-coil state to a random semi-compact globule. It then proceeds by a slow, rate-determining search through the semi-compact states to find a transition state from which the chain folds rapidly to the native state. The elements of the folding mechanism that lead to the resolution of the Levinthal paradox are the reduced number of conformations that need to be searched in the semi-compact globule (approximately 10(10) versus approximately 10(16) for the random coil) and the existence of many (approximately 10(3)) transition states. The results have evolutionary implications and suggest principles for the folding of real proteins.

Models, Chemical↗
PubMed1994

The contribution of vibrational entropy to molecular association. The dimerization of insulin.

The association reaction of two molecules to form a single complex must overcome a large entropic barrier due to the loss of translational and rotational degrees of freedom; estimates of the T delta S term are of the order of 30 kcal/mol for proteins. The approach of Chandler and Pratt is used to provide a statistical mechanical formulation for the connection between the gas-phase and solution binding free energies. This makes possible a clear separation of the vibrational contribution to the gas-phase binding enthalpy and entropy from the solvation terms. Further, it suggests that the calculated gas-phase result, should be a good approximation in solution for many systems. To illustrate the formulation, a harmonic dynamics model is used to study the dimerization of insulin. The vibrational entropy increase in the dimer complex, relative to the two separate monomers, is 23 entropy units. This contributes -7.2 kcal/mol to the dimerization free energy. It is not possible to identify a small number of specific dimer modes that give rise to this entropy contribution. Instead, small alterations in the frequencies of many modes below 400 to 600 cm-1 are found to contribute. The relative importance of vibrational and other effects in macromolecule-macromolecule and macromolecule-small molecule associations is discussed.

Binding Sites↗
PubMed1994

Molecular recognition in proteins. Simulation analysis of substrate binding by a tyrosyl-tRNA synthetase mutant.

Alchemical molecular dynamics simulations are performed to determine the difference in the free energy of binding of the tyrosine substrate between the wild type of tyrosyl-tRNA synthetase (TyrRS) from Bacillus stearothermophilus and the mutant Tyr169-->Phe. The results are of general interest because the Tyr169 hydroxyl group interacts with the ammonium group of the substrate in a manner corresponding to that found in other amino acid binding proteins (e.g. the Asp receptor of the chemotactic bacterium Salmonella typhimurium and class I major histocompatibility complex molecules). The calculated free-energy change due to the Tyr169-->Phe mutation is 3.4 kcal/mol (the statistical error is +/- 0.5 kcal/mol) in satisfactory agreement with the experimental value of 3(+/- 0.5) kcal/mol. By use of thermodynamic integration, the contribution of the different terms to the free energy change are estimated. The path dependence of such a decomposition is discussed and it is suggested that the alchemical choice is of primary interest for understanding the interactions involved. There are large protein contributions to the alchemical free energy difference of the bound and free enzyme that cancel in the overall result. Due to this cancellation, the essential interactions contributing to the free-energy change are those between the OH group of Tyr169 and water in the free enzyme and those between the OH group of Tyr169 and the ammonium group of the substrate in the bound system. The results thus support simple models based on a balance of hydrogen bonding interactions.

Bacterial Proteins↗
PubMed1994

Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase.

The transition in barnase from the native state to a compact globule has been studied with high-temperature molecular dynamics simulations. A partial destruction of the alpha-helices and the outer strands of the beta-sheet is observed with water molecules replacing the hydrogen bonds of the secondary structural elements. Simultaneously, the main alpha-helix moves away from the beta-sheet and exposes the principal hydrophobic core, many of whose nonpolar side chains, beginning with the ones near the surface, become solvated by hydrogen-bonded water molecules. This step involves a significant increase in the solvent-exposed surface area; the resulting loss of stability due to the hydrophobic effect may be the major source of the activation barrier in the unfolding reaction. The detailed mechanism described here for the first stage of the denaturation of barnase, including the essential role of water molecules, is likely to be representative of protein denaturation, in general.

Bacillus↗
PubMed1994

Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.

A three-dimensional lattice model of a protein is used to investigate the properties required for its folding to the native state. The polypeptide chain is represented as a 27 bead heteropolymer whose lowest energy (native) state can be determined by an exhaustive enumeration of all fully compact conformations. A total of 200 sequences with random interactions are generated and subjected to Monte Carlo simulations to determine which chains find the ground state in a short time; i.e. which sequences overcome the folding problem referred to as the Levinthal paradox. Comparison of the folding and non-folding sequences is used to identify the features that are required for fast folding to the global energy minimum. It is shown that successful folding does not require certain attributes that have been previously proposed as necessary for folding; these include a high number of short versus long-range contacts in the native state, a high content of the secondary structure in the native state, a strong correlation between the native contact map and the interaction parameters, and the existence of a high number of low energy states with near-native conformation. Instead, the essential difference between the folding and the non-folding sequences is the nature of the energy spectrum. The necessary and sufficient condition for a sequence to fold rapidly in the present model is that the native state is a pronounced energy minimum. As a consequence, the thermodynamic stability of the native state of a folding sequence has a sigmoidal dependence on temperature. This permits such a sequence to satisfy both the thermodynamic and the kinetic requirements for folding; i.e. the native state predominates thermodynamically at temperatures that are high enough for folding to be kinetically possible. The applicability of the present results to real proteins is discussed.

Algorithms↗
PubMed1994

Protein folding dynamics: the diffusion-collision model and experimental data.

The diffusion-collision model of protein folding is assessed. A description is given of the qualitative aspects and quantitative results of the diffusion-collision model and their relation to available experimental data. We consider alternative mechanisms for folding and point out their relationship to the diffusion-collision model. We show that the diffusion-collision model is supported by a growing body of experimental and theoretical evidence, and we outline future directions for developing the model and its applications.

Diffusion↗
PubMed1994

HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site.

A program (HOOK) is described for generating potential ligands that satisfy the chemical and steric requirements of the binding region of a macromolecule. Functional group sites with defined positions and orientations are derived from known ligand structures or the multicopy simulation search (MCSS) method (Miranker, A., Karplus, M. Proteins 11:29-34, 1991). HOOK places molecular "skeletons" from a database into the protein binding region by making bonds between sites ("hooks") on the skeleton and functional groups. The nonpolar interactions with the binding region of candidate molecules are assessed by use of a simplified van der Waals potential. The method is illustrated by constructing ligands for the sialic acid binding site of the hemagglutinin from the influenza A virus and the active site of chloramphenicol acetyltransferase. Aspects of the HOOK program that lead to a highly efficient search of 10(5) or more skeletons for binding to 10(2) or more functional group minima are outlined.

Algorithms↗
PubMed1994

Free energy simulations: the meaning of the individual contributions from a component analysis.

A theoretical analysis is made of the decomposition into contributions from individual interactions of the free energy calculated by thermodynamic integration. It is demonstrated that such a decomposition, often referred to as "component analysis," is meaningful, even though it is a function of the integration path. Moreover, it is shown that the path dependence can be used to determine the relation of the contribution of a given interaction to the state of the system. To illustrate these conclusions, a simple transformation (Cl- to Br- in aqueous solution) is analyzed by use of the Reference Interaction Site Model-Hypernetted Chain Closure integral equation approach; it avoids the calculational difficulties of macromolecular simulation while retaining their conceptual complexity. The difference in the solvation free energy between chloride and bromide is calculated, and the contributions of the Lennard-Jones and electrostatic terms in the potential function are analyzed by the use of suitably chosen integration paths. The model is also used to examine the path dependence of individual contributions to the double free energy differences (delta delta G or delta delta A) that are often employed in free energy simulations of biological systems. The alchemical path, as contrasted with the experimental path, is shown to be appropriate for interpreting the effects of mutations on ligand binding and protein stability. The formulation is used to obtain a better understanding of the success of the Poisson-Boltzmann continuum approach for determining the solvation properties of polar and ionic systems.

Bromides↗