Biomedical subjects

J Walshaw

Publications and source records attributed to J Walshaw.

5 recordsLinked to original sources

PubMed2001

Socket: a program for identifying and analysing coiled-coil motifs within protein structures.

The coiled coil is arguably the simplest protein-structure motif and probably the most ubiquitous facilitator of protein-protein interactions. Coiled coils comprise two or more alpha-helices that wind around each other to form "supercoils". The hallmark of most coiled coils is a regular sequence pattern known as the heptad repeat. Despite this apparent simplicity and relatedness at the sequence level, coiled coils display a considerable degree of structural diversity: the helices may be arranged parallel or anti-parallel and may form a variety of oligomer states. To aid studies of coiled coils, we developed SOCKET, a computer program to identify these motifs automatically in protein structures. We used SOCKET to gather a set of unambiguous coiled-coil structures from the RCSB Protein Data Bank. Rather than searching for sequence features, the algorithm recognises the characteristic knobs-into-holes side-chain packing of coiled coils; this proved to be straightforward to implement and was able to distinguish coiled coils from the great majority of helix-helix packing arrangements observed in globular domains. SOCKET unambiguously defines coiled-coil helix boundaries, oligomerisation states and helix orientations, and also assigns heptad registers. Structures retrieved from the Protein Data Bank included parallel and anti-parallel variants of two, three and four-stranded coiled coils, one example of a parallel pentamer and a small number of structures that extend the classical description of a coiled coil. We anticipate that our structural database and the associated sequence data that we have gathered will be of use in identifying principles for coiled-coil assembly, prediction and design. To illustrate this we give examples of sequence and structural analyses of the structures that are possible using the new data bases, and we present amino acid profiles for the heptad repeats of different motifs.

Algorithms↗

PubMed2001

Guidelines for the assembly of novel coiled-coil structures: alpha-sheets and alpha-cylinders.

The coiled coil is a ubiquitous motif that guides many different protein-protein interactions. The accepted hallmark of coiled coils is a seven-residue (heptad) sequence repeat. The positions of this repeat are labelled a-b-c-d-e-f-g, with residues at a and d tending to be hydrophobic. Such sequences form amphipathic alpha-helices, which assemble into helical bundles via knobs-into-holes interdigitation of residues from neighbouring helices. We wrote an algorithm, SOCKET, to identify this packing in protein structures, and used this to gather a database of coiled-coil structures from the Protein Data Bank. Surprisingly, in addition to commonly accepted structures with a single, contiguous heptad repeat, we identified sequences with multiple, offset heptad repeats. These 'new' sequence patterns help to explain oligomer-state specification in coiled coils. Here we focus on the structural consequences for sequences with two heptad repeats offset by two residues, i.e. a/f'-b/g'-c/a'-d/b'-e/c'-f/d'-g/e'. This sets up two hydrophobic seams on opposite sides of the helix formed. We describe how such helices may combine to bury these hydrophobic surfaces in two different ways and form two distinct structures: open 'alpha-sheets' and closed 'alpha-cylinders'. We highlight these with descriptions of natural structures and outline possibilities for protein design.

Animals↗

PubMed2001

Open-and-shut cases in coiled-coil assembly: alpha-sheets and alpha-cylinders.

The coiled coil is a ubiquitous protein-folding motif. It generally is accepted that coiled coils are characterized by sequence patterns known as heptad repeats. Such patterns direct the formation and assembly of amphipathic alpha-helices, the hydrophobic faces of which interface in a specific manner first proposed by Crick and termed "knobs-into-holes packing". We developed software, SOCKET, to recognize this packing in protein structures. As expected, in a trawl of the protein data bank, we found examples of canonical coiled coils with a single contiguous heptad repeat. In addition, we identified structures with multiple, overlapping heptad repeats. This observation extends Crick's original postulate: Multiple, offset heptad repeats help explain assemblies with more than two helices. Indeed, we have found that the sequence offset of the multiple heptad repeats is related to the coiled-coil oligomer state. Here we focus on one particular sequence motif in which two heptad repeats are offset by two residues. This offset sets up two hydrophobic faces separated by approximately 150 degrees -160 degrees around the alpha-helix. In turn, two different combinations of these faces are possible. Either similar or opposite faces can interface, which leads to open or closed multihelix assemblies. Accordingly, we refer to these two forms as alpha-sheets and alpha-cylinders. We illustrate these structures with our own predictions and by reference to natural variants on these designs that have recently come to light.

Amino Acid Motifs↗

PubMed1995

Solvent interactions with pi ring systems in proteins.

The interaction of water molecules with apolar amino acids is an important aspect of the hydrophobic effect and hence of protein folding. Our distributed multiple electrostatic model for water interacting with phenylalanine dipeptides shows that minimum energy sites exist above the aromatic ring such that a solvent molecule can interact with the pi electrons, but only when this site is not blocked by main-chain atoms or disturbed by main-chain polar atoms. This is consistent with the experimental evidence of others that water can hydrogen bond to aromatic pi electrons. In contrast, our analysis of solvent interactions with phenylalanine residues based on 48 high-resolution, well-refined protein structures shows that the dominant interaction of solvent molecules is with the edge of the ring and not with the pi elections. As the faces of phenylalanine rings tend to be buried, and solvent interactions with neighbouring polar atoms are more favourable, the interaction of water molecules with the faces of aromatic pi rings appears not to occur frequently in proteins.

Crystallography↗

PubMed1993

Distribution of solvent molecules around apolar side-chains in protein crystals.

We have analysed the distribution of solvent sites within 5.0 A of the apolar side-chains alanine, valine, leucine, isoleucine and phenylalanine based on experimental data from 24 high-resolution protein structures. Clustering of solvent molecules into specific regions can be seen superimposed on a broad background of sites. The non-random nature of these distributions is confirmed by quantitative analysis of the solvent sites according to a spherical polar (r, theta and phi) co-ordinate system with the apolar atom of interest at the centre. One of the general features of these solvent sites is that they peak at around 4.0 A from an apolar protein carbon atom. Preferences in orientation (theta and phi) are also seen in the solvent distributions especially around the alanine CB atom and the phenylalanine ring. Most (around 75%) of the solvent sites around apolar groups are also within hydrogen bonding distance of protein (main chain) polar groups which leads to a distribution dependent on the local secondary structure. The remaining 25% of solvent sites are referred to as "non-polar" water molecules and their crystallographic temperature factors are higher than average by between 15% to 28%. For alanine and phenylalanine there are enough data to show that water molecules not within hydrogen bonding distance of protein polar atoms also cluster into specific regions. However, the main conclusion appears to be that the hydrophobic hydration in protein crystals is correlated with hydration of polar groups and thus depends on the local environment as well as on the stereochemistry of the apolar atoms.

Alanine↗