Showing papers on "Structural biology published in 1997"

Folding dynamics and mechanism of β-hairpin formation

Abstract: Protein chains coil into α-helices and β-sheet structures. Knowing the timescales and mechanism of formation of these basic structural elements is essential for understanding how proteins fold1. For the past 40 years, α-helix formation has been extensively investigated in synthetic and natural peptides2,3,4,5, including by nanosecond kinetic studies6,7. In contrast, the mechanism of formation of β structures has not been studied experimentally. The minimal β-structure element is the β-hairpin, which is also the basic component of antiparallel β-sheets. Here we use a nanosecond laser temperature-jump apparatus to study the kinetics of folding a β-hairpin consisting of 16 amino-acid residues. Folding of the hairpin occurs in 6 µs at room temperature, which is about 30 times slower than the rate of α-helix formation6,7. We have developed a simple statistical mechanical model that provides a structural explanation for this result. Our analysis also shows that folding of a β-hairpin captures much of the basic physics of protein folding, including stabilization by hydrogen bonding and hydrophobic interactions, two-state behaviour, and a funnel-like, partially rugged energy landscape.

Distant homology recognition using structural classification of proteins

Abstract: Protein structure prediction is arguably the biggest unsolved problem of structural biology. The notion of the number of naturally occurring different protein folds being limited allows partial solution of this problem by the use of fold recognition methods, which "thread" the sequence in question through a library of known protein folds. The fold recognition methods were thought to be superior to the distant homology recognition methods when there is no significant sequence similarity to known structures. We show here that the Structural Classification of Proteins (SCOP) database, organizing all known protein folds according their structural and evolutionary relationships, can be effectively used to enhance the sensitivity of the distant homology recognition methods to rival the "threading" methods. In the CASP2 experiment, our approach correctly assigned into existing SCOP superfamilies all of the six "fold recognition" targets we attempted. For each of the six targets, we correctly predicted the homologous protein with a very similar structure; often, it was the most similar structure. We correctly predicted local alignments of the sequence features that we found to be characteristic for the protein superfamily containing a given target. Our global alignments, extended manually from these local alignments, also appeared to be rather accurate.

An account of NMR in structural biology.

Abstract: With the ability to determine atomic resolution structures of biological macromolecules in semi-physiological conditions, nuclear magnetic resonance spectroscopy (NMR) has become an eminent tool in structural biology. NMR provides a means for studying critical biological phenomena including protein structure, dynamics and folding as well as a practical approach to drug design.

The T-cell receptor as immunoglobulin: paradigm regained

Abstract: The quest to determine the molecular nature of T-lymphocyte receptors for antigen was a "holy grail" to immunologists for over 25 years. This paper updates a review written 15 years ago (Marchalonis JJ, Hunt JC. Proc Soc Exp Biol Med 171:127-145, 1982), which proposed that "these molecules apparently do not bear determinants specified by the major histocompatibility complex, but express Ig-related variable regions and constant regions unique to T-cell products." We review subsequent contributions from molecular biology, protein chemistry, peptide immunochemistry, and structural biology establishing that T-cell receptors (TCRs) are members of the immunoglobulin family restricted to T cells that share 3-dimensional structural features, sequence homology, antigenic cross-reactivity, and common mechanisms of diversification with conventional immunoglobulins. These molecules and their light- and heavy-chain siblings appeared contemporaneously in vertebrate evolution with the emergence of sharks. We illustrate how extrapolation of concepts from immunoglobulin to T-cell receptors has aided in the understanding of these often enigmatic molecules, and, conversely, how concepts derived for T-cell receptors such as the role of "superantigens" can be directly applied to conventional immunoglobulins. A second precept that follows from the symmetry of the combining sites of Igs and TCRs is that MHC-restricted antibodies should exist. Such molecules have in fact been reported, and the x-ray crystallography for T-cell receptors suggests that the combining sites recognizing simultaneously MHC and peptide epitopes resemble the combining sites of antibodies directed against protein determinants. Additional immunoglobulin molecules of nonmammalian species have been detected and characterized based upon conserved homology to TCR and Igs, and it is anticipated that further study will enable the identification of more antigen-specific members of the family in mammals as well.

Promise: a new database of information on prosthetic centres and metal ions in protein active sites.

Abstract: The PROMISE (Prosthetic centres and metal ions in protein active sites) database aims to gather together comprehensive sequence, structural, functional and bibliographic information on proteins which possess prosthetic centres, with an emphasis on active site structure and function. The database is available on the World Wide Web at http://bioinf.leeds.ac.uk/promise/ BACKGROUND Of the more than 5000 proteins of known three-dimensional structure, at least half contain metal ions or other non-protein prosthetic groups in their active sites; such prosthetic groups often themselves containing metal ions. Nature has made abundant use of the wide range of chemical properties of the elements, exemplified conspicuously by the complex coordination states of the transition metals. The presence of metal ions and other prosthetic groups confers vitally important properties on the proteins concerned, while the protein environments of the groups modulate the chemistry of the ions in subtle ways. The ‘tuning’ of the chemical reactivity of catalytic centres to the needs of the organism by this interplay of the protein and non-protein components is clearly highly sensitive to the local geometry of the active sites and further modified by the overall molecular structure. The genome sequencing and other structural biology projects are accumulating ever more data, but the need to systematise and analyse the data becomes correspondingly more demanding. In addition to the rapidly growing ‘primary’ databanks of nucleic acid and protein sequences (corresponding already to >150 000 different proteins) and the Protein Databank of three-dimensional (3-D) structures, a number of ‘secondary’ databases have been derived, covering a diverse array of specialised areas. These include classification of proteins in terms of invariant active site groups (3), of ‘fingerprints’ of complex sequence motifs ( 1) or of patterns of chain fold ( 13,19). The PROMISE database is uniquely focused on protein active site structure and on the relationships between protein molecules and non-protein prosthetic centres, combining the relevant sequence, 3-D structural and physico-chemical information (7). The concept of bioinorganic motif (14), a structural feature peculiar for metalloproteins and other complex proteins, may be useful in further discussion. Bioinorganic motifs, some of which are exemplified in Figure 1, endow a protein with function(s) possessed by neither the apoprotein nor prosthetic group alone. These motifs are quite different from sequence motifs (basically strings of text) or protein fold motifs (such as βαβ or HTH motifs). Although there are many families of proteins sharing both fold and bioinorganic motif, there are also evolutionarily unrelated but functionally analogous systems which have similar bioinorganic motif and, vice versa, there are proteins which share the same fold but have distinct active site structures. Bioinorganic motifs often possess unique spectroscopic properties which make it possible to study them relatively independently from the rest of the protein matrix.

Protein signature analysis: a practical new approach for studying structure-activity relationships in peptides and proteins.

Abstract: Publisher Summary This chapter presents a new approach for studying structure-activity relationships in peptides and proteins. The emergence of new techniques in structural biology and molecular biology has greatly improved the ability to study the molecular basis of protein function. These approaches are complementary in the type of information they provide: a high-resolution protein structure often suggests the generation of site mutants of the protein to test the validity of structure-based hypotheses. It introduces a new technique, protein signature analysis (PSA) that provides a more rapid route to the systematic modification (of the covalent structure) and analysis of a peptide or protein. This approach takes advantage of the chemical synthesis. Protein signature analysis is a chemistry-driven method that provides a functional profile of the effects of structure variation throughout a peptide or protein sequence. The technique integrates advances in the total chemical synthesis of proteins and biomolecular mass spectrometry s into a practical new tool for studying structure-activity relationships in peptides and small proteins.