Biomedical subjects

G Vriend

Publications and source records attributed to G Vriend.

106 records · Page 6Linked to original sources

PubMed1990

WHAT IF: a molecular modeling and drug design program.

A FORTRAN 77 computer program has been written to aid with macromolecular modeling and drug design. Called WHAT IF, it provides an intelligent and flexible environment for displaying, manipulating, and analyzing small molecules, proteins, nucleic acids, and their interactions. A relational protein structure database is incorporated to be queried. The program is suitable for most common crystallographic work. The menu-driven operation of WHAT IF, combined with the use of default values wherever user input is required, makes it very easy to use for a novice user while keeping full flexibility for more sophisticated studies. Although there are not too many unique features in WHAT IF, the fact that everything is integrated in one program makes it a unique tool for many purposes.

Computer Graphics↗

PubMed1990

Contribution of the C-terminal amino acid to the stability of Bacillus subtilis neutral protease.

The role of the C-terminal Leu300 in maintaining thermal stability of the neutral protease of Bacillus subtilis was investigated. From model building studies based on the three-dimensional structure of thermolysin, the neutral protease of B. thermoproteolyticus, it was concluded that this residue is located in a hydrophobic pocket composed of residues located in the C-terminal and the middle domain. To test the hypothesis that Leu300, by contributing to a stabilizing interaction between these domains, is important for enzyme stability, several neutral protease mutants were constructed and characterized. The thermostability of the enzyme was lowered by deleting Leu300 or by replacing this residue by a smaller (Ala), a polar (Asn) or a sterically unfavourable (Ile) amino acid. Thermostability was increased upon replacing Leu300 by Phe. These results are in agreement with model-building studies. The effects on thermostability observed after mutating the corresponding Val318 in the thermostable neutral protease of B.stearothermophilus were less pronounced.

Amino Acid Sequence↗

PubMed1990

Parameter relation rows: a query system for protein structure function relationships.

In the course of molecular modeling or mutant prediction one often wants quick answers to questions such as: 'Are there any residues in a beta-strand that point into an internal cavity, and are highly mutable?' 'Are there large polar residues in a helix that make a contact with a hydrophobic residue in a sheet, and don't make the maximal number of hydrogen bonds?' or 'Which hydrophobic residues are in a helix with a large hydrophobic moment, and make a contact with a co-factor, but at the same time still have a large accessible surface?'. I describe here a method to get answers to these kinds of questions in a very quick and easy manner. The method described is partly based on the principles used in the design of relational databases, and its mode of operation is similar to the query methods used in a relational database environment. Although designed for aiding in molecular modeling, its applicability is much more general. The method has been implemented as part of a large molecular modeling package which copes with the numerous problems in systematic handling of protein structures, e.g. residue numbering. This also implies that many normal tools such as graphical analyses, I/O facilities, etc. are available on-line.

Databases, Factual↗

PubMed1989

Crystal structure of the p-hydroxybenzoate hydroxylase-substrate complex refined at 1.9 A resolution. Analysis of the enzyme-substrate and enzyme-product complexes.

Using synchrotron radiation, the X-ray diffraction intensities of crystals of p-hydroxy-benzoate hydroxylase, complexed with the substrate p-hydroxybenzoate, were measured to a resolution of 1.9 A. Restrained least-squares refinement alternated with rebuilding in electron density maps yielded an atom model of the enzyme-substrate complex with a crystallographic R-factor of 15.6% for 31,148 reflections between 6.0 and 1.9 A. A total of 330 solvent molecules was located. In the final model, only three residues have deviating phi-psi angle combinations. One of them, the active site residue Arg44, has a well-defined electron density and may be strained to adopt this conformation for efficient catalysis. The mode of binding of FAD is distinctly different for the different components of the coenzyme. The adenine ring is engaged in three water-mediated hydrogen bonds with the protein, while making only one direct hydrogen bond with the enzyme. The pyrophosphate moiety makes five water-mediated versus three direct hydrogen bonds. The ribityl and ribose moieties make only direct hydrogen bonds, in all cases, except one, with side-chain atoms. The isoalloxazine ring also makes only direct hydrogen bonds, but virtually only with main-chain atoms. The conformation of FAD in p-hydroxybenzoate hydroxylase is strikingly similar to that in glutathione reductase, while the riboflavin-binding parts of these two enzymes have no structural similarity at all. The refined 1.9 A structure of the p-hydroxybenzoate hydroxylase-substrate complex was the basis of further refinement of the 2.3 A structure of the enzyme-product complex. The result was a final R-factor of 16.7% for 14,339 reflections between 6.0 and 2.3 A and an improved geometry. Comparison between the complexes indicated only small differences in the active site region, where the product molecule is rotated by 14 degrees compared with the substrate in the enzyme-substrate complex. During the refinements of the enzyme-substrate and enzyme-product complexes, the flavin ring was allowed to bend or twist by imposing planarity restraints on the benzene and pyrimidine ring, but not on the flavin ring as a whole. The observed angle between the benzene ring and the pyrimidine ring was 10 degrees for the enzyme-substrate complex and 19 degrees for the enzyme-product complex. Because of the high temperature factors of the flavin ring in the enzyme-product complex, the latter value should be treated with caution. Six out of eight peptide residues near the flavin ring are oriented with their nitrogen atom pointing towards the ring.(ABSTRACT TRUNCATED AT 400 WORDS)

4-Hydroxybenzoate-3-Monooxygenase↗

PubMed1989

X-ray structure of lipoamide dehydrogenase from Azotobacter vinelandii determined by a combination of molecular and isomorphous replacement techniques.

The crystal structure of lipoamide dehydrogenase from Azotobacter vinelandii has been determined by a combination of molecular replacement and isomorphous replacement techniques yielding eventually a good-quality 2.8 A electron density map. Initially, the structure determination was attempted by molecular replacement procedures alone using a model of human glutathione reductase, which has 26% sequence identity with this bacterial dehydrogenase. The rotation function yielded the correct orientation of the model structure both when the glutathione reductase dimer and monomer were used as starting model. The translation function could not be solved, however. Consequently, data for two heavy-atom derivatives were collected using the Hamburg synchotron facilities. The derivatives had several sites in common, which was presumably a major reason why the electron density map obtained by isomorphous information alone was of poor quality. Application of solvent flattening procedures cleaned up the map considerably, however, showing clearly the outline of the lipoamide dehydrogenase dimer, which has a molecular weight of 100,000. Application of the "phased translation function", which combines the phase information of both isomorphous and molecular replacement, led to an unambiguous determination of the position of the model structure in the lipoamide dehydrogenase unit cell. The non-crystallographic 2-fold axis of the dimer was optimized by several cycles of constrained-restrained least-squares refinement and subsequently used for phase improvement by 2-fold density averaging. After ten cycles at 3.5 A, the resolution was gradually extended to 2.8 A in another 140 cycles. The 2.8 A electron density distribution obtained in this manner was of much improved quality and allowed building of an atomic model of A. vinelandii lipoamide dehydrogenase. It appears that in the orthorhombic crystals used each dimer is involved in contacts with eight surrounding dimers, leaving unexplained why the crystals are rather fragile. Contacts between subunits within one dimer, which are quite extensive, can be divided into two regions separated by a cavity. In one of the contact regions, the level of sequence identity with glutathione reductase is very low but it is quite high in the other. The folding of the polypeptide chain in each subunit is quite similar to that of glutathione reductase, as is the extended conformation of the co-enzyme FAD.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed1989

Structure determination of Mengo virus.

The structure of Mengo virus was determined to 3.0 A resolution using human rhinovirus 14 as an initial phasing model at 8.0 A resolution. Oscillation diffraction photographs were collected at the Cornell High Energy Synchrotron Source using orthorhombic Mengo virus crystals. The crystal space group was P2(1)2(1)2(1), a = 441.4, b = 427.3 and c = 421.9 A, with one icosahedral particle per asymmetric unit, giving 60-fold noncrystallographic redundancy. The orientations of the four viral particles in the unit cell were determined with a rotation function. Their positions relative to the crystallographic symmetry axes were found by a combination of Patterson-function analysis and a subsequent R-factor search using human rhinovirus 14 atomic coordinates as a model. The initial phases to 8.0 A resolution were then computed by placing human rhinovirus 14 particles in the orientations and positions of Mengo virus particles. These phases were improved by ten cycles of real-space molecular replacement averaging. Phases between 8.0 and 3.0 A resolution were obtained by molecular replacement phase extension. One or two reciprocal-space lattice points were used for each extension followed by two cycles of averaging.

Crystallization↗

PubMed1989

Trypsin sensitivity of several human rhinovirus serotypes in their low pH-induced conformation.

Five serotypes of human rhinovirus (HRV) were examined for sensitivity to trypsin at physiological pH, HRV1A, HRV2, and HRV14 were found to be resistant whereas in serotypes HRV49 and HRV89 degradation of VP2 was observed. However, exposure to low pH followed by neutralization, a treatment which causes irreversible conformational changes in the capsid, led to rapid cleavage by trypsin of VP1 in HRV1A, HRV2, and HRV49 at defined sites followed by degradation of VP2. In the case of HRV2, the cleavage site in VP1 was determined by direct protein sequencing and was shown to occur between Arg260 and Thr261, close to the C-terminus. HRV49 behaves similarly to HRV2 as expected from extensive sequence similarity in this region, whereas VP1 in HRV1A is most probably cleaved at a site closer to the C-terminus than that in HRV2. Although HRV14 contains the same amino acid pair present in HRV2 and HRV49, it was not cleaved under these conditions. HRV89, which lacks a basic residue at the corresponding position, was also insensitive. Examination of the cleavage site on the three-dimensional structural map of native HRV2 reveals that it is most probably buried inside the capsid and thus not accessible. Structural rearrangements of the viral capsid are thus necessary to account for the cleavage observed after low pH treatment.

Capsid↗

PubMed1989

A very fast program for visualizing protein surfaces, channels and cavities.

A method for visualizing molecular surfaces is described that uses a grid to store the distance to the nearest atom. Using on-the-fly three-dimensional (3D) contouring of a molecular graphics program such as FRODO, one can obtain a good impression of van der Waals surfaces and solvent-accessible surfaces. The main advantages of the method described here are its high speed and the fact that no recalculations need to be done to obtain the solvent-accessible surface visualized for a probe with another radius.

Algorithms↗

PubMed1987

The atomic structure of Mengo virus at 3.0 A resolution.

The structure of Mengo virus, a representative member of the cardio picornaviruses, is substantially different from the structures of rhino- and polioviruses. The structure of Mengo virus was solved with the use of human rhinovirus 14 as an 8 A resolution structural approximation. Phase information was then extended to 3 A resolution by use of the icosahedral symmetry. This procedure gives promise that many other virus structures also can be determined without the use of the isomorphous replacement technique. Although the organization of the major capsid proteins VP1, VP2, and VP3 of Mengo virus is essentially the same as in rhino- and polioviruses, large insertions and deletions, mostly in VP1, radically alter the surface features. In particular, the putative receptor binding "canyon" of human rhinovirus 14 becomes a deep "pit" in Mengo virus because of polypeptide insertions in VP1 that fill part of the canyon. The minor capsid peptide, VP4, is completely internal in Mengo virus, but its association with the other capsid proteins is substantially different from that in rhino- or poliovirus. However, its carboxyl terminus is located at a position similar to that in human rhinovirus 14 and poliovirus, suggesting the same autocatalytic cleavage of VP0 to VP4 and VP2 takes place during assembly in all these picornaviruses.

Antigens, Viral↗

PubMed1987

Comparison of the three-dimensional structure of two human rhinoviruses (HRV2 and HRV14).

An attempt has been made to build a model of human rhinovirus 2 (HRV2) based on the known human rhinovirus 14 (HRV14) structure. HRV2 was selected because its amino acid sequence is known and because it belongs to the minor rhinovirus receptor class as compared to HRV14, which belongs to the major class. Initial alignment of HRV2 with HRV14 based on the primary sequence and the knowledge of the three-dimensional structure of HRV14 showed that the most probable position of the majority of insertions and deletions occurred in the vicinity of the neutralizing immunogenic sites (NIm). Out of a total of 855 amino acids present in one copy of each of the capsid proteins VP1 through VP4 of HRV14, 411 are different between the two viruses. There are also 6 amino acid residues inserted and 14 residues deleted in HRV2 relative to HRV14. Examination of amino acid interactions showed several cases of conservation of function, e.g., salt bridges or the filling of restricted space. The largest variation amongst the residues lining the canyon, the putative receptor binding site, was in the carboxy-terminal residues of VP1.

Amino Acid Sequence↗

PubMed1987

Implications of the picornavirus capsid structure for polyprotein processing.

Mature picornaviral proteins are derived by progressive, posttranslational cleavage of a precursor polyprotein. These cleavages play a role in the control of virus functions. Although the processed termini are separated by as much as 75 A in the native virus capsid, the fold and arrangement of polypeptide chains in a protomer before proteolysis are likely to be similar to that found in the mature virus. The three-dimensional structures of rhinovirus and Mengo virus suggest that the cleavage sites within the protomeric precursor are in structurally flexible regions. The final proteolytic processing event, maturation of the virion peptide VP0 (also called peptide 1AB) appears to occur by an unusual autocatalytic serine protease-type mechanism possibly involving viral RNA basic groups that would serve as proton-abstractors during the cleavage reaction.

Capsid↗

PubMed1986

Role of the N-terminal part of the coat protein in the assembly of cowpea chlorotic mottle virus. A 500 MHz proton nuclear magnetic resonance study and structural calculations.

The interaction of the oligonucleotides (Ap)8A and (A-T)5 with empty capsids of the coat protein of cowpea chlorotic mottle virus (CCMV) has been studied with 500 MHz 1H nuclear magnetic resonance. It is found that these oligonucleotides specifically bind to the arginine and lysine residues of the N-terminal arm of the protein. Upon this binding, immobilization of part of the N-terminal arm occurs. In addition, secondary structure predictions and energy calculations have been performed on the N-terminal arm. These calculations were carried out as a function of the charges on the arginine and lysine side-chains. For free coat protein, where the arginine and lysine side-chains are charged, the arm is found in a random-coil conformation. In the neutralized state, as for the coat protein in the virus, the arm adopts an alpha-helical conformation. The results support a previously published model for the assembly of CCMV, in which a random-coil to alpha-helix conformational transition, induced by neutralizing the arginine and lysine side-chains, plays an essential role.

Amino Acid Sequence↗

PubMed1986

The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating.

WIN 51711 and WIN 52084 are structurally related, antiviral compounds that inhibit the replication of rhino (common cold) viruses and related picornaviruses. They prevent the pH-mediated uncoating of the viral RNA. The compounds consist of a 3-methylisoxazole group that inserts itself into the hydrophobic interior of the VP1 beta-barrel, a connecting seven-membered aliphatic chain, and a 4-oxazolinylphenoxy group (OP) that covers the entrance to an ion channel in the floor of the "canyon." Viral disassembly may be inhibited by preventing the collapse of the VP1 hydrophobic pocket or by blocking the flow of ions into the virus interior.

Antiviral Agents↗

PubMed1982

Prediction of secondary structural elements in the phosphatidylcholine-transfer protein from bovine liver.

Secondary structural elements of the phosphatidylcholine-transfer protein from bovine liver have been predicted from its primary structure with the aid of two computerized methods. The predicted alpha-helix and beta-strand content have been compared with the values derived from circular dichroism spectra. The hydrophobicity profile (Rose plot) of the protein indicated that the supposed lipid-binding site occurs in the most hydrophobic region. The predicted secondary structural elements have been folded in a tentative model of the protein molecule according to its hydrophobicity profile.

Amino Acid Sequence↗

PubMed1979

Kinetic analysis of the interaction of the phosphatidylcholine exchange protein with unilamellar vesicels and multilamellar liposomes.

The mode of action of the phosphatidylcholine exchange protein from bovine liver has been studied by using unilamellar vesicles and multilamellar liposomes both of which membranes contain phosphatidylcholine and phosphatidic acid. The protein-mediated exchange of phosphatidylcholine between vesicles and liposomes fit the kinetic model presented in a previous study [V.D. Besselaar et al. (1975) Biochemistry, 1j, 1852]. Kinetic analysis of the rates of exchange indicate that the apparent dissociation constant of the exchange protein-vesicle complex decreases with an increasing phosphatidic acid content of the vesicles. Both vesicles and liposomes of 10 mol% phosphatidic acid show the same dissociation constant; on the other hand, both the formation and the disruption of the protein-membrane complex was 50--100-times higher for the vesicles than for the liposomes. This implies that the exchange protein can discriminate between vesicles and liposomes. Equilibrium gel chromatography of a column of Bio Gel A-5m confirmed that the exchange protein binds more strongly to vesicles of an increased phosphatidic acid content. The protein-mediated exchange of phosphatidylcholine in the vesicle-liposome system demonstrates a pH optimum at 4.0 to 5.5. The kinetic analysis at pH 5.0 as compared to pH 7.4 indicates that the enhanced exchange at pH 5.0 can solely be accounted for by altered interaction of the exchange protein with the liposomes.

Carrier Proteins↗

PubMedDate not supplied

Full window stereo.

Visualisation is the bioinformaticist's most important tool for the study of macromolecules, and being able to see molecules in stereo is a crucial aspect. Stereo vision is based on the principle that each eye is presented with the best possible image of what it would have seen if the object was really there in 3D. The simplest approach to stereo vision is to display the right eye picture on the right half of the screen and the left eye picture on the left half while using a mirror system to ensure that each eye sees what it is supposed to see. More expensive workstations use hardware to alternately display the left and right eye pictures while synchronously blocking the transparency in the right or left lens of the special glasses worn by the user. We present here some simple software that uses inexpensive hardware, originally designed for the computer game industry, to make full screen stereo available on Linux-based PCs. The quality of the stereo vision is similar to the top-of-the-line graphics workstations that are capable of quad-buffering. This stereo option has been incorporated in the XII based version of WHAT IF (Vriend, G. J. Mol. Graphics 1990, 8, 52-56), but the stereo source code is freely available and can easily be incorporated in other visualization packages.

Humans↗