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A Kidera

Publications and source records attributed to A Kidera.

31 records · Page 2Linked to original sources
PubMed1995

Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide.

A Monte Carlo simulation method for globular proteins, called extended-scaled-collective-variable (ESCV) Monte Carlo, is proposed. This method combines two Monte Carlo algorithms known as entropy-sampling and scaled-collective-variable algorithms. Entropy-sampling Monte Carlo is able to sample a large configurational space even in a disordered system that has a large number of potential barriers. In contrast, scaled-collective-variable Monte Carlo provides an efficient sampling for a system whose dynamics is highly cooperative. Because a globular protein is a disordered system whose dynamics is characterized by collective motions, a combination of these two algorithms could provide an optimal Monte Carlo simulation for a globular protein. As a test case, we have carried out an ESCV Monte Carlo simulation for a cell adhesive Arg-Gly-Asp-containing peptide, Lys-Arg-Cys-Arg-Gly-Asp-Cys-Met-Asp, and determined the conformational distribution at 300 K. The peptide contains a disulfide bridge between the two cysteine residues. This bond mimics the strong geometrical constraints that result from a protein's globular nature and give rise to highly cooperative dynamics. Computation results show that the ESCV Monte Carlo was not trapped at any local minimum and that the canonical distribution was correctly determined.

Algorithms↗
PubMed1994

Functional analysis and modeling of a conformationally constrained Arg-Gly-Asp sequence inserted into human lysozyme.

To examine the effect of a conformational constraint introduced into the Arg-Gly-Asp (RGD) sequence on cell adhesion activity, we have constructed mutant proteins by inserting RGD-containing sequences flanked by two Cys residues between Val74 and Asn75 of human lysozyme. CRGDC-, CRGDSC-, and CGRGDSC-inserted mutant lysozymes were expressed in yeast, purified, and designated as Cys-RGD3, Cys-RGD4, and Cys-RGD5, respectively. In baby hamster kidney cells, these mutants were shown to possess high cell adhesion activity by interaction with vitronectin receptor (integrin alpha v beta 3), and this activity is 2-3-fold higher than that of the RGDS-inserted mutant lysozyme, RGD4. The mutant proteins also inhibited the binding of human fibrinogen to its receptor (integrin alpha IIb beta 3) at a lower concentration than the RGD4 protein. Peptide mapping and mass spectrometric analyses showed that the two inserted Cys residues in these mutants are linked to each other without any effects on the mode of the four disulfide bonds present in native human lysozyme. These results suggest that the introduction of a conformational constraint into the RGD region significantly increases the cell adhesion activity. The conformation of the RGD region in Cys-RGD4 was modeled by a Monte Carlo simulation. Most of the sampled conformations were grouped into three classes; the first is characterized by an extended Gly conformation, the second assumes a type II' beta turn, and the third has a salt bridge between Arg and Asp.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1994

Response of dynamic structure to removal of a disulfide bond: normal mode refinement of C77A/C95A mutant of human lysozyme.

In order to investigate the response of dynamic structure to removal of a disulfide bond, the dynamic structure of human lysozyme has been compared to its C77A/C95A mutant. The dynamic structures of the wild type and mutant are determined by normal mode refinement of 1.5-A-resolution X-ray data. The C77A/C95A mutant shows an increase in apparent fluctuations at most residues. However, most of the change originates from an increase in the external fluctuations, reflecting the effect of the mutation on the quality of crystals. The effects of disulfide bond removal on the internal fluctuations are almost exclusively limited to the mutation site at residue 77. No significant change in the correlation of the internal fluctuations is found in either the overall or local dynamics. This indicates that the disulfide bond does not have any substantial role to play in the dynamic structure. A comparison of the wild-type and mutant coordinates suggests that the disulfide bond does not prevent the 2 domains from parting from each other. Instead, the structural changes are characteristic of a cavity-creating mutation, where atoms surrounding the mutation site move cooperatively toward the space created by the smaller alanine side chain. Although this produces tighter packing, more than half of the cavity volume remains unoccupied, thus destabilizing the native state.

Binding Sites↗
PubMed1994

Determinants of protein side-chain packing.

The problem of protein side-chain packing for a given backbone trace is investigated using 3 different prediction models. The first requires an exhaustive search of all possible combinations of side-chain conformers, using the dead-end elimination theorem. The second considers only side-chain-backbone interactions, whereas the third neglects side-chain-backbone interactions and instead keeps side-chain-side-chain interactions. Predictions of side-chain conformations for 11 proteins using all 3 models show that removal of side-chain-side-chain interactions does not cause a large decrease in the prediction accuracy, whereas the model having only side-chain-side-chain interactions still retains a significant level of accuracy. These results suggest that the 2 classes of interactions, side-chain-backbone and side-chain-side-chain, are consistent with each other and work concurrently to stabilize the native conformations. This is confirmed by analyses of energy spectra of the side-chain conformations derived from the fourth prediction model, the Independent model, which gives almost the same quality of the prediction as the dead-end elimination. The analyses indicate that the 2 classes of interactions simultaneously increase the energy difference between the native and nonnative conformations.

Algorithms↗
PubMed1994

Collective motions in proteins investigated by X-ray diffuse scattering.

We have developed theoretical models for analysis of X-ray diffuse scattering from protein crystals. A series of models are proposed to be used for experimental data with different degrees of precision. First, we propose the normal mode model, where conformational dynamics of a protein is assumed to occur mostly in a limited conformational subspace spanned by a small number of low-frequency normal modes in the protein. When high precision data are available, variances and covariances of the normal mode variables can be determined from experimental data using this model. For experimental data with lower degrees of precision, we introduce a series of simpler models. These models express the covariance matrix using relatively simple empirical correlation functions by assuming the correlation between a pair of atoms to be isotropic. As an application of these simpler models, we calculate diffuse-scattering patterns from a human lysozyme crystal to examine how each adjustable parameter in the models affects general features of the resulting patterns. The results of the calculation are summarized as follows. (1) The higher order scattering makes a significant contribution at high resolutions. (2) The resulting simulated patterns are sensitive to changes in correlation lengths of about 1 A, as well as to changes of the functional form of the correlation function. (3) But only the "average" value of the intra- and intermolecular correlation lengths seems to determine the gross features of the pattern. (4) The effect of the atom-dependent amplitude of fluctuations is difficult to observe.

Computer Simulation↗
PubMed1994

Dynamic structure of human lysozyme derived from X-ray crystallography: normal mode refinement.

X-ray crystallography provides a wealth of information about the dynamic as well as static protein structure. A new method of dynamic structure refinement of protein X-ray crystallography, normal mode refinement, is proposed. In this method, the Debye-Waller factor is expanded in terms of the low-frequency internal normal modes and external normal modes, whose amplitudes and couplings are optimized in the process of crystallographic refinement. The internal and external contributions to the atomic fluctuations can be separated. Also, anisotropic atomic fluctuations and their inter-atomic correlations can be determined experimentally even with a relatively small number of adjustable parameters. The method is applied to the analyses of experimental data of human lysozyme and its mutant, C77A/C95A, to reveal its dynamic structure.

Crystallography, X-Ray↗
PubMed1993

Intrinsic nature of the three-dimensional structure of proteins as determined by distance geometry with good sampling properties.

A protocol for distance geometry calculation is shown to have excellent sampling properties in the determination of three-dimensional structures of proteins from nuclear magnetic resonance (NMR) data. This protocol uses a simulated annealing optimization employing mass-weighted molecular dynamics in four-dimensional space (Havel, T.F. (1991) Prog. Biophys. Mol. Biol., 56, 43-78). It attains an extremely large radius of convergence, allowing a random coil conformation to be used as the initial estimate for the succeeding optimization process. Computations are performed with four systems of simulated distance data as tests of the protocol, using an unconstrained L-alanine 30mer and three different types of proteins, bovine pancreatic trypsin inhibitor, the alpha-amylase inhibitor Tendamistat, and the N-terminal domain of the 434-repressor. The test of the unconstrained polypeptide confirms that the sampled conformational space is that of the statistical random coil. In the larger and more complicated systems of the three proteins, the protocol gives complete convergence of the optimization without any trace of initial structure dependence. As a result of an exhaustive conformational sampling by the protocol, the intrinsic nature of the structures generated with distance restraints derived from NMR data has been revealed. When the sampled structures are compared with the corresponding X-ray structures, we find that the averages of the sampled structures always show a certain pattern of discrepancy from the X-ray structure. This discrepancy is due to the short distance nature of the distance restraints, and correlates with the characteristic shape of the protein molecule.

Animals↗
PubMed1992

Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data.

A dynamic structure refinement method for X-ray crystallography, referred to as the normal mode refinement, is proposed. The Debye-Waller factor is expanded in terms of the low-frequency normal modes whose amplitudes and eigenvectors are experimentally optimized in the process of the crystallographic refinement. In this model, the atomic fluctuations are treated as anisotropic and concerted. The normal modes of the external motion (TLS model) are also introduced to cover the factors other than the internal fluctuations, such as the lattice disorder and diffusion. A program for the normal mode refinement (NM-REF) has been developed. The method has first been tested against simulated diffraction data for human lysozyme calculated by a Monte Carlo simulation. Applications of the method have demonstrated that the normal mode refinement has: (1) improved the fitting to the diffraction data, even with fewer adjustable parameters; (2) distinguished internal fluctuations from external ones; (3) determined anisotropic thermal factors; and (4) identified concerted fluctuations in the protein molecule.

Humans↗
PubMed1992

Normal mode refinement: crystallographic refinement of protein dynamic structure. II. Application to human lysozyme.

The dynamic structure of a protein, human lysozyme, is determined by the normal mode refinement of X-ray crystal structure. This method uses the normal modes of both internal and external motions to distinguish the real internal dynamics from the external terms such as lattice disorder, and gives an anisotropic and concerted picture of atomic fluctuations. The refinement is carried out with diffraction data of 5.0 to 1.8 A resolution, which are collected on an imaging plate. The results of the refinement show: (1) Debye-Waller factor consists of two parts, highly anisotropic internal fluctuations and almost isotropic external terms. The former is smaller than the latter by a factor of 0.72 in the scale of B-factor. Therefore, the internal dynamics cannot be recognized directly from the apparent electron density distribution. (2) The internal fluctuations show basically similar features as those predicted by the normal mode analysis, with almost the same amplitude and a similar level of anisotropy. (3) Correlations of fluctuations are detected between two lobes forming the active site cleft, which move simultaneously in opposite directions. This corresponds to the hinge-bending motion of lysozyme.

Humans↗
PubMed1992

Normal mode refinement: crystallographic refinement of protein dynamic structure applied to human lysozyme.

A new method of dynamic structure refinement of protein x-ray crystallography, normal mode refinement, is developed. In this method the Debye-Waller factor is expanded in terms of the low-frequency normal modes and external normal modes, whose amplitudes and couplings are optimized in the process of crystallographic refinement. By this method, internal and external contributions to the atomic fluctuations can be separated. Also, anisotropic atomic fluctuations and their interatomic correlations can be determined experimentally even with a relatively small number of adjustable parameters. The method is applied to the analysis of experimental data of human lysozyme to reveal its dynamic structure.

Humans↗
PubMed1990

Refinement of protein dynamic structure: normal mode refinement.

An x-ray crystallographic refinement method, referred to as the normal mode refinement, is proposed. The Debye-Waller factor is expanded in terms of the effective normal modes whose amplitudes and eigenvectors are experimentally determined by the crystallographic refinement. In contrast to the conventional method, the atomic motions are treated generally as anisotropic and concerted. This method is assessed by using the simulated x-ray data given by a Monte Carlo simulation of human lysozyme. In this article, we refine the dynamic structure by fixing the average static structure to exact coordinates. It is found that the normal mode refinement, using a smaller number of variables, gives a better R factor and more information on the dynamics (anisotropy and collectivity in the motion).

Mathematics↗
PubMed1988

Cluster analysis of amino acid indices for prediction of protein structure and function.

The relationship among 222 published indices representing various physicochemical and biochemical properties of amino acid residues has been investigated by hierarchical cluster analysis. The clustering result is illustrated by the minimum spanning tree, which is conveniently divided into four regions: alpha and turn propensities, beta propensity, hydrophobicity and other physicochemical properties including, among others, bulkiness of amino acid residues. In addition, several subclasses of hydrophobicity scales have been identified: preference of inside and outside, accessible surface area, surrounding hydrophobicity and other mostly experimental scales including transfer free energy, partition coefficients, HPLC parameters and polarity. Representative amino acid indices are identified in each of these groups. The collection of amino acid indices is a useful resource for empirical analyses correlating sequence information with structural and functional properties of proteins. As an example, the indices that best reproduce the amino acid mutation data matrix are searched against this collection.

Amino Acids↗