Simulation of oligopeptide dynamics and folding. The use of NMR chemical shifts to analyse the MD trajectories.

In this paper, a simulation of the folding process, based on a random perturbations of the phi, psi, chi1 dihedral angles, is proposed to approach the formation at the atom level of both principal elements of protein secondary structure, the alpha-helix and the beta-hairpin structures. Expecting to understand what may happen in solution during the formation of such structures, the behaviour of large sets of random conformations that are generated for small oligopeptides was analysed. Different factors that may influence the folding (as conformational propensity, hydrophobic interactions and side-chain mobility) were investigated.

The use of NMR chemical shifts to analyse the MD trajectories: simulation of bovine pancreatic trypsin inhibitor dynamics in water as a test case for solvent influences.

In this paper the NMR secondary chemical shifts, that are estimated from a set of 3D-structures, are compared with the observed ones to appraise the behaviour of a known x-ray diffraction structure (of the bovine pancreatic trypsin inhibitor protein) when various molecular dynamics are applied. The results of a 200 ps molecular dynamics under various conditions are analysed and different ways to modify the molecular dynamics are considered. With the purpose of avoiding the time-consuming explicit representation of the solvent (water) molecules, an attempt was made to understand the role of the solvent and to develop an implicit representation, which may be refined.

Influence of thermal motion on 1H chemical shifts in proteins: the case of bovine pancreatic trypsin inhibitor.

The possible influence of thermal motion on 1H chemical shifts is discussed for a small stable protein, the bovine pancreatic Kunitz trypsin inhibitor (BPTI). The thermal effects on the aromatic side chains and on the backbone are treated separately. The thermal motion of the aromatic side chains is accounted for in terms of their rotation around the C(alpha)-C(beta) bond and the motion of each individual proton is interpreted as a ratio between the amount of ordered and quite disordered states.

Synthesis and CD studies of an 88-residue peptide containing the main receptor binding site of HTLV-I SU-glycoprotein.

Essential HTLV-1 biological functions, like host-cell receptor recognition, depend on the structural motives on the surface glycoprotein gp46. We defined a peptide of 88 amino acids [Arg147-Leu234] corresponding to the central part of the protein sequence, where major neutralizing epitopes are localized. After evaluating the feasibility of its chemical synthesis, the chosen sequence was realized using the stepwise solid-phase methodology.

Constrained refinement based on NOE and chemical shift information: the monomer form of arginine-vasopressin-like insect factor.

Via the refinement process of the monomer form of an arginine-vasopressin-like insect factor, the paper analyses the most relevant NMR information to define the solution structure of a flexible peptide. The relative importance of the different NOE constraints is discussed.

The use of proton chemical shifts to define the solution structure of a dimeric peptide.

For flexible peptides, nuclear Overhauser Effects (NOE) experiments do not provide enough information to ensure a correct definition of their solution structure. The use of distance constraints, derived from the knowledge of proton chemical shifts, is developed to restrict the number of possible conformations. In the case of flexible molecules, randomization appears as an important factor of the correct estimation of the chemical shifts from the 3D structure.

Recognition by human sera of a variable region of the surface glycoprotein of HTLV-I.

The region comprised between the amino acids 175 and 199 of the HTLV-I envelope surface glycoprotein is one of the immunodominant domains of this molecule. In this region, which is well recognized by sera from HTLV-I infected patients, a substitution of the proline at position 192 by a serine has been described in some isolates. Because this mutation could modify the secondary structure of the glycoprotein molecule, we studied the inference of the presence of proline or serine on the recognition of the region 175-199 by human sera.

The catalytic domain of endoglucanase A from Clostridium cellulolyticum: effects of arginine 79 and histidine 122 mutations on catalysis.

Sequence analysis of the endoglucanase EGCCA of Clostridium cellulolyticum indicates the existence of two domains: a catalytic domain extending from residue 1 to residue 376 and a reiterated domain running from residue 390 to 450. A small deletion in the C terminal end of the catalytic domain inactivated the protein. From the analysis of the sequences of 26 endoglucanases belonging to family A, we focused on seven amino acids which were totally conserved in all the catalytic domains compared.

Sequence variability of bovine leukemia virus env gene and its relevance to the structure and antigenicity of the glycoproteins.

The nucleotide sequences of the env genes of seven bovine leukemia viruses and the encoded peptide sequence were compared, with the objective of (i) determining the genetic distance separating bovine leukemia virus isolates from different geographical regions, (ii) identifying particular amino acids that contribute to the sequential and conformational epitopes, and (iii) relating such epitopes to their projected position in a three-dimensional model of the structure of the gp51 surface glycoprotein. Two bovine leukemia virus subgroups were clearly identified, a Japanese-American subgroup represented by strains lambda BLV-1, VdM, and FLK-BLV and a European subgroup by strains T15-2, LB285, and LB59. It was possible to identify amino acids that were important in determining three of the epitopes (F, G, and H) recognized by neutralizing monoclonal and polyclonal antibodies.

The use of folding patterns in a multisolution approach of the all-beta protein three-dimensional structure. A beta-roll structure is predicted in the retroviral glycoprotein.

An automatic macromolecular modelling package of unknown protein structures was developed using the intimate correlation which appears between the observed X-ray structures and their associated predicted folding patterns. The method can be considered as a generalization of both the combinatorial [1] and the template identification [2,3] approaches which were proposed some years ago, and provide a fast way of selecting 'structural motifs' to build new proteins. As an illustration, the tertiary fold of the all-beta-domain of the retroviral outermembrane glycoprotein is proposed.

The use of folding patterns in the search of protein structural similarities; a three-dimensional model of phosphoribosyl transferases.

A new way to predict the topologies of proteins of unknown three-dimensional structure is derived from the comparison of the distribution of the strongest predicted secondary structures with equivalent distributions recorded for proteins of known X-ray structures. As an illustration the tentative three-dimensional model of phosphoribosyl transferases which was proposed by Argos et al. is rediscussed.

The use of folding patterns in the prediction of protein topologies.

We proved previously that the distribution of formation energies which may be associated with the predicted secondary structures (or nuclei) is specific of the folding process (Busetta, B. 1986, Biochim. Biophys.

Examination of folding patterns for predicting protein topologies.

From the prediction of protein secondary structures, formation energies may be estimated for each incipient nucleus of the folding process. The averaging which may be performed on large families of distantly related proteins improves the accuracy of measurement of these energies and the efficiency of the prediction of the different steps involved in the protein folding (secondary structures, domain boundaries, topologies, etc.) and allows the description of new folding patterns.

The prediction of protein domains.

The ab initio prediction of the domain boundaries and types remains one of the most important problems which makes a possible description of protein tertiary structure from its amino-acid sequence elusive. The present paper describes new methods to predict both of them. The predictions of domain boundaries and types in proteins of known X-ray structures are reported in order to check the efficiency of these new algorithms.

The prediction of protein topologies.

The estimates of the different contributions to the free energy of folded proteins are derived from analysis of protein X-ray structures, and introduced in the conformational analysis of the protein tertiary structures at a very macroscopic level. Different predictions of protein topologies are reported in the case of all-alpha and all-beta proteins.