“Topohydrophobic positions” as key markers of globular protein folds

The positions of a given fold always occupied by strong hydrophobic amino acids (V, I, L, F, M, Y, W), which we call “topohydrophobic positions”, were detected and their properties demonstrated within 153 non-redundant families of homologous domains, through 3D structural alignments. Sets of divergent sequences possessing at least four to five members appear to be as informative as larger sets, provided that their mean pairwise sequence identity is low. Amino acids in topohydrophobic positions exhibit several interesting features: they are much more buried than their equivalents in non-topohydrophobic positions, their side chains are far less dispersed; and they often constitute a lattice of close contacts in the inner core of globular domains. In most cases, each regular secondary structure possesses one to three topohydrophobic positions, which cluster in the domain core. Moreover, using sensitive alignment processes such as hydrophobic cluster analysis (HCA), it is possible to identify topohydrophobic positions from only a small set of divergent sequences. Amino acids in topohydrophobic positions, which can be identified directly from sequences, constitute key markers of protein folds, define long-range structural constraints, which, together with secondary structure predictions, limit the number of possible conformations for a given fold. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 16 November 1998     

Deciphering globular protein sequence–structure relationships: from observation to prediction

Careful comparison of proteins sharing a same fold but only low or no sequence identity should allow a better understanding of the coding of three-dimensional structures by amino acid sequences. It has already been shown that positions of a given fold occupied mainly by hydrophobic residues in the different proteins of a structural family share very specific physical properties and participate in stabilization of the protein domain. They probably also play a crucial role in the very first steps of folding [ Poupon A, Mornon J.-P (1999) FEBS Lett. 452: 283–289; Mirny LA, Shaknovich EI (1999) J. Mol. Biol. 291: 177–196]. To further understand the sequence–structure relationship, we studied the correlation between allowed mutations at a given three-dimensional position and some of its physical properties. The different amino acids were divided in three groups (hydrophobic, nonpolar or weakly polar and polar or charged), and a correlation was established between the occupation rate of each group at a given position in the fold and the burying, the side-chain dispersion, the interposition distances and the ability to form a network of directly interacting residues. The results are then applied to predict some solvent accessibility. We show that this property can be accurately predicted for about 70% of the residues, providing precious information concerning the corresponding three-dimensional structures. The results are used to predict other structural features, as secondary structures, compactness or long-range interactions between residues remote in sequence. This information will allow the number of possible structures for a given sequence to be reduced considerably, simplifying the ab initio modelling problem to a level where it might be solved by computing methods. Received: 7 October 2000 / Accepted: 5 January 2001 / Published online: 3 April 2001     

Common prevalence of alanine and glycine in mobile reactive centre loops of serpins and viral fusion peptides: Do prions possess a fusion peptide?

Summary Serpin reactive centre loops and fusion peptides released by proteolytic cleavage are particularly mobile. Their amino acid compositions reveal a common and unusual abundance of alanine, accompanied by high levels of glycine. These two small residues, which are not simultaneously abundant in stable helices (standard or transmembrane), probably play an important role in mobility. Threonine and valine (also relatively small amino acids) are also abundant in these two kinds of peptides. Moreover, the known 3D structures of an uncleaved serpin reactive centre and a fusion peptide are strikingly similar. Such sequences possess many small residues and are found in several signal peptides and in PrP, a protein associated with spongi-form encephalopathies and resembling virus envelope proteins. These properties may be related to the infection mechanisms of these diseases.     

Thiophene 1-oxides. V. Comparison of the crystal structures and thiophene ring aromaticity of 2,5-diphenylthiophene,its sulfoxide and sulfone

The detailed preparation of 2,5-diphenylthiophene 1-oxide (2) is reported as well as the comparative study of the crystal structures of 2,5-diphenylthiophene, 1 , its sulfoxide 2 and sulfone 3 obtained by X-ray diffraction. This work represents the first experimental study of a complete heterocyclic series, including a thiophene derivative, and the corresponding sulfoxide and sulfone. On the basis of the geometrical parameters, the first unequivocal experimental parameters obtained for a thiophene 1-oxide derivative, we have also examined the evolution of the aromatic character of the thiophene ring when oxidizing the sulfur atom to the sulfoxide and the sulfone. Paolini's bond orders and Julg and Francois's aromaticity indices have also been calculated for the three compounds and compared to those previously calculated for related thiophene derivatives by semi-empirical or ab initio methods [6], [7]. All the data examined showed that, in spite of its non planarity, the thiophene ring of 2,5-diphenylthiophene 1-oxide 2 could still exhibit some de localization of its p electrons indicating a certain degree of aromaticity lower than in thiophene 1 but higher than in the sulfone 3 .