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O Tapia

Publications and source records attributed to O Tapia.

At least 37 records · Page 2Linked to original sources
PubMed1991

A molecular dynamics study of a model built Pro-36-Gly mutant derived from the potato carboxypeptidase A inhibitor protein.

A 120ps molecular dynamics (MD) trajectory was calculated and analyzed for a putative Pro-36-Gly mutant of the potato carboxypeptidase A (CPA) protein inhibitor (PCIm). The mutant protein's fold shows a large degree of stability, judged from its low alpha-carbon r.m.s. deviation from the X-ray structure of the wild type PCI (PCIw). The N-terminal tail of PCIm differs slightly less from the X-ray structure than it does in PCIw, while the mutant's C-terminal tail (the primary contact site with CPA) and residues 13-17 present deviations as they approach each other. Differences in fluctuation pattern exist between PCIm and PCIw in residues 2-4 (the N-terminal tail), 13-17, 22-23, 28-31 (the secondary contact site with CPA) and 37-38 (the C-terminal tail); the latter region is rigidified in PCIm. Results show that the MD method is able to sense local perturbative effects produced by amino acid substitutions in flexible regions of protein molecules. The simulation suggests that the conformation of the C-terminal tail is less favorable for interaction with the target protein in the mutant than it is in the wild type protein. The Pro-36-Gly mutant is predicted to be a less potent inhibitor.

Carboxypeptidases↗
PubMed1991

Implementing knot-theoretical characterization methods to analyze the backbone structure of proteins: application to CTF L7/L12 and carboxypeptidase A inhibitor proteins.

In this work we apply a recently developed method for characterizing the shape of the tertiary structure of proteins. The approach is based on a combination of graph- and knot-theoretical characterizations of Cartesian projections of the space curve describing the protein backbone. The proposed technique reduces the essential shape features to a topologically based code formed by a sequence of knot symbols and polynomials. These polynomials are topological invariants that describe the overcrossing and knotting patterns of curves derived from the molecular space curve. These descriptors are algorithmically computed. The procedure is applied to describe the structure of the carboxy terminal fragment of the L7/L12 chloroplast ribosomal protein (CTF L7/L12) and the potato carboxypeptidase A inhibitor protein (PCI), which has a set of three disulfide bridges. In the former case, we describe the protein's shape features in terms of its alpha-helices, and a backbone simplified by considering helices without internal structure. An extension of the methodology to describe disulfide bridges is discussed and applied to PCI. Changes in the knot-theoretical characterization due to possible uncertainties in the resolution of the X-ray structure, as well as the inclusion of low-frequency motions of the backbone, are also discussed.

Carboxypeptidases↗
PubMed1990

Structure and fluctuations of bacteriophage T4 glutaredoxin modelled by molecular dynamics.

A 120 ps molecular dynamics (MD) trajectory for bacteriophage T4 glutaredoxin was calculated including non-inertial solvent effects. The potential energy attains an equilibrated regime after the first 20 ps. The r.m.s. difference of all non-hydrogen atoms between X-ray and average MD structures for the regular secondary structure is 0.99A which shows that the MD simulation reproduces the essentials of the structure with high accuracy. Loop displacements are detected, shown by the larger full structure all non-hydrogen atom r.m.s. difference of 1.2A. The fluctuation pattern derived from MD agrees fairly well with that derived from X-ray isotropic temperature factors. The active site is a stable structural region in this MD modellization. Structural changes are put in context with the protein's function.

Amino Acid Sequence↗
PubMed1990

Molecular volumes and surfaces of biomacromolecules via GEPOL: a fast and efficient algorithm.

A triangular tesselation approach to build up surfaces has been adapted to the study of biomolecules. By using a data-coded generic pentakisdodecahedron each atom is assigned a particular sphere whose radii are chosen according to any suitable property. Different types of surfaces have been adapted to this method: van der Waals, surface accessible, and Richard's molecular surface. A simple method is used to eliminate all triangles found at the intersection volume of the atomic spheres and a fast algorithm is employed to calculate the area of the envelope surface and the volume therein. The data about the surface are given by the coordinates of the center of each triangle, elementary surface value, and vector coordinates of the normal to the surface. Color coding of standard properties such as charge densities, potential energy, or any scalar property can be easily done with standard graphics libraries. Fairly detailed information on vector properties, such as electric field and atom velocity, can also be graphically represented by using projections along the normals with adequate color coding.

Algorithms↗
PubMed1989

A molecular dynamics study of the C-terminal fragment of the L7/L12 ribosomal protein. II. Effects of intermolecular interactions on structure and dynamics.

The crystallographic dimer of the C-terminal fragment (CTF) of the L7/L12 ribosomal protein has been subjected to molecular dynamics (MD) simulations. A 90 picosecond (ps) trajectory for the protein dimer, 19 water molecules and two counter ions has been calculated at constant temperature. Effects of intermolecular interactions on the structure and dynamics have been studied. The exact crystallographic symmetry is lost and the atomic fluctuations differ from one monomer to the other. The average MD structure is more stable than the X-ray one, as judged by accessible surface area and energy calculations. Crystal (non-dimeric) interactions have been simulated in another 40 ps trajectory by using harmonic restraints to represent intermolecular hydrogen bonds. The conformational changes with respect to the X-ray structure are then virtually suppressed. The unrestrained dimer trajectory has been scanned for cooperative motions involving secondary structure elements. The intrinsic collective motions of the monomer are transmitted via intermolecular contacts to the dimer structure. The existence of a stable dimeric form of CTF, resembling the crystallographic one, has been documented. At the cost of fairly small energy expenditure the dimer has considerable conformational flexibility. This flexibility may endow the dimer with some functional potential as an energy transducer.

Computer Simulation↗
PubMed1987

Aspects of model building applied to the C-terminal domain of the L12 protein from chloroplast ribosomes: a molecular dynamics study.

A 170 picosecond molecular dynamics trajectory has been calculated starting from a model-built structure of chloroplast CTF. Local conformational changes occur during the equilibration period. Thereafter, a dynamically stable structure is attained. The conformational changes involve a turn connecting two structural subdomains which has an amino acid insertion and several substitutions with respect to the E. coli sequence. Potential energy minimisation alone fails to detect such a change. The overall folding and atomic positional fluctuations are very similar to those found in MD simulations of the E. coli molecule. The combined use of computer graphics based model building and MD calculations has lead to a thermally stable putative structure for the chloroplast CTF.

Chemical Phenomena↗
PubMed1986

Molecular dynamics simulations of the holo and apo forms of retinol binding protein. Structural and dynamical changes induced by retinol removal.

The effects of removing retinol from the X-ray structure of holo-retinol binding protein are studied using the molecular dynamics technique. Structural and dynamical properties emerging from an 80 ps simulation of the apo form, for which no crystallographic structure is available, are compared with the results of a 70 ps trajectory of the holo-protein. Dynamical stationarity is attained after roughly 30 ps, and the resulting average structure is proposed as a reasonable model of the apo-protein. Conformational changes are observed for the loops at the beta-barrel entrance during the non-equilibrium part of the apo-trajectory. Tryptophan labelling experiments and retinoid reconstitution experiments point towards this part of the molecule as being involved in prealbumin binding. Structural changes in this region may therefore explain the differences in prealbumin affinity between the apo and holo forms. Furthermore, a change in the position of the alpha-helix, corresponding to a pivot around its C terminus, is observed for the apo-protein. The resulting conformation of the alpha-helix is found to be similar to that in apo-beta-lactoglobulin, which also can bind retinol and for which a crystal structure exists. The results from the holo simulation are compared to the crystallographic data and show good agreement. The dynamics of the secondary and tertiary structural elements are analysed and compared for the two forms. The beta-barrel is found to be extremely cooperative in its atomic motions in both simulations, and the top and bottom beta-sheets perform collective fluctuations with respect to each other in the low-frequency limit of the simulations. The dynamics of the alpha-helical region presents clear differences between the two forms; while the holo-protein has a well-defined spectrum for the longitudinal stretching mode, the apo form displays a fairly large bending of the alpha-helix at several points of the trajectory.

Computer Simulation↗
PubMed1986

Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode.

A study of the hinge bending mode in the enzyme liver alcohol dehydrogenase is made by use of empirical energy functions. The enzyme is a dimer, with each monomer composed of a coenzyme binding domain and a catalytic domain with a large cleft between the two. Superposition of the apoenzyme and holoenzyme crystal structures is used to determine a rigid rotation axis for closing of the cleft. It is shown that a rigid body transformation of the apoenzyme to the holoenzyme structure corresponds to a 10 degrees rotation of the catalytic domain about this axis. The rotation is not along the least-motion path for closing of the cleft but instead corresponds to the catalytic domain coming closer to the coenzyme binding domain by a sliding motion. Estimation of the energy associated with the interdomain motion of the apoenzyme over a range of 90 degrees (-40 to 50 degrees, where 0 degrees corresponds to the minimized crystal structure) demonstrates that local structural relaxation makes possible large-scale rotations with relatively small energy increments. A variety of structural rearrangements associated with the domain motion are characterized. They involve the hinge region residues that provide the covalent connections between the two domains and certain loop regions that are brought into contact by the rotation. Differences between the energy minimized and the holoenzyme structures point to the existence of alternative conformations for loops and to the importance of the ligands in the structural rearrangements.

Alcohol Dehydrogenase↗
PubMed1986

Structural changes in retinol binding protein induced by retinol removal. A molecular dynamics study.

Relationships between structure and function for retinol binding protein (RBP) are elucidated with help of a 2.0 A resolution X-ray structure of the holo-protein and an average molecular dynamics (MD) structure of the apo-form. Comparisons between MD simulations of both the apo- and holo-forms with the X-ray holo-structure show conformational changes in apo-RBP that may be functionally significant. The average three dimensional structure obtained for apo-RBP is compared to the related protein apo-beta-lactoglobulin. Available biochemical information is consistent with structure/function relationships derived here.

Humans↗
PubMed1986

The catalytic mechanism of serine proteases. III. An Indo-ISCRF study of the methylacetate docking in alpha-chymotrypsin.

Mechanistic steps of the catalytic hydrolysis of methylacetate by alpha-chymotrypsin have been studied with the inhomogeneous selfconsistent reaction field theory of protein core effects. Protein-substrate interactions were optimized at each step of the reaction path by using the REFINE program. The state of charge of the acid and basic side chains together with the amino terminal group have been used to mimic pH effects. The experimental facts concerning the catalytic activity are fairly well reproduced in our simulations. In particular, the trends in activation barrier as a function of pH are good, although the actual energetic barriers are much too large.

Acetates↗
PubMed1986

On the molecular mechanism of liver alcohol dehydrogenase: Monte Carlo simulations and X-ray studies of water in the substrate channel.

Water structure in the substrate channel of liver alcohol dehydrogenase as a function of the oxidation state of the coenzyme nicotinamide ring has been studied with Monte Carlo simulations. X-ray data on water structure has been analyzed. The simulations show an order-disorder effect in the water distribution produced by the charge state of the ring; also, solvation-desolvation effects are detected. For positively charged ring, the water molecules form a fluctuated H-bonded network that connects the deeply buried active site zinc to the bulk solvent. This network together with the side chain of Ser-48 most likely is the support for a proton relay system thereby providing a mechanism responsible of the pKa shift of the zinc-bound water as it is produced by the oxidized coenzyme binding.

Alcohol Dehydrogenase↗
PubMed1985

A molecular dynamics study of the C-terminal fragment of the L7/L12 ribosomal protein. Secondary structure motion in a 150 picosecond trajectory.

A 150 picosecond molecular dynamics computer simulation of the C-terminal fragment of the L7/L12 ribosomal protein from Escherichia coli is reported. The molecular dynamics results are compared with the available high-resolution X-ray data in terms of atomic positions, distances and positional fluctuations. Good agreement is found between the molecular dynamics results and the X-ray data. The form and parameters of the interaction potential energy function and the procedures for deriving it are discussed. Some current misunderstandings concerning the ways of evaluating the efficiency of molecular dynamics algorithms and of application of bond-length constraints in protein simulations are cleared up. The 150 picosecond trajectory has been scanned in a search for correlated motions within and between secondary structure elements. The beta-strands have diffusional stretching modes, and uncorrelated transversal displacements. The dynamic analysis of alpha-helices shows a variety of features. The atomic fluctuations differ between the helix ends; this effect reflects long time-scale motions. Two alpha-helices, alpha A and alpha C, show diffusive longitudinal stretching modes. The third helix, alpha B, has a correlated asymmetric longitudinal stretching; the N-terminal part dominates this behaviour. Furthermore, alpha B presents a librational motion with respect to the other parts of the molecule with a frequency of approximately 5 cm-1. This motion is coupled to helix stretching. Interestingly, the regions of highly conserved residues contain the most mobile parts of the molecule.

Bacterial Proteins↗
PubMed1985

The catalytic mechanism of serine proteases II: The effect of the protein environment in the alpha-chymotrypsin proton relay system.

The proton relay system of alpha-chymotrypsin is analyzed by the INDOISCRF method. The effects of the protein electric and polarization fields are explicitly introduced in the calculations. It is shown that the multicharged structure Ser-His+Asp- is the most sensitive, from an energetic view-point, towards the protein surrounding effects. Variations in the permanent and polarization fields are discussed, as well as the influence of the substrate and one water molecule localized in the active site of the enzyme. The catalytic role of such changes is conjectured.

Binding Sites↗
PubMedDate not supplied

Proteins in vacuo: denaturing and folding mechanisms studied with computer-simulated molecular dynamics.

Mounting evidence from experiments suggests that the native fold in solution is metastable in dehydrated proteins. Results from a number of experiments that use mass spectrometry indicate also that folding-unfolding transitions take place in protein ions even in the absence of water. These observations on anhydrous proteins call for a re-evaluation of our understanding of the folding transition. In this context, computer-assisted simulations are an important complementary tool. Here, we provide an overview of recent progress on the simulation of proteins in vacuo. In particular, we discuss the response of proteins and protein ions to perturbations that trigger unfolding and re-folding transitions. By comparing the general patterns emerging from theory and experiment, we propose a series of new measurements that could help to validate, and improve, current simulation models.

Algorithms↗