Showing papers by "Chris Sander published in 1979"

Antiparallel and parallel β-strands differ in amino acid residue preferences

Abstract: A β-strand is a particular type of extended sequence of amino acid residues, an element of secondary structure of proteins. β-sheets are an assembly of strands, often bringing together parts of the protein which are separated along the backbone. As such, β-sheets are an element of tertiary structure. Parallel βP) and antiparallel (βA) arrangements of strands in a sheet differ in the hydrogen bond pattern between strands, as shown schematically in Fig. 1, and in the type of chain connectivity they allow: short reverse turn connections for βA and longer crossover connections for βP (refs 1–3). Most present secondary structure prediction methods (for reviews refs 4–6) use a four-state distinction of secondary structure: α-helix, β-strand or extended, reverse turn, and ‘random coil’ (everything else). With a data base of 30–40 different protein structures, the conformational preferences for all amino acid residues in these four states seem to have converged7. However, the steadily increasing data base of structurally known proteins makes a refinement of the four-state description feasible. Although more refined classifications of conformational states based on finer subdivisions of (φ,Ψ)-space have been made8,9, we prefer making distinctions based on structural environment. Using a novel definition of β-sheet structure in terms of the tertiary structure juxtaposition of strands, we have analysed residue contacts in known β-sheets and report here secondary structure preferences for the 20 amino acids, separately for antiparallel and parallel arrangements of strands. The distinction between the two arrangements results in strikingly different and sharpened sets of preference parameters, including some of the largest values reported so far for any substructure. These results point the way towards a basic improvement of secondary structure predictions by further distinction of secondary structure elements according to tertiary structure environment. Beyond secondary structure prediction, the different preferences for βA and βP may aid in predicting the tertiary interaction between strands.

Degeneracy of the information contained in amino acid sequences: evidence from overlaid genes.

Abstract: The observed gene overlays in the viruses ФX174 and SV40 show a surprising economy of information storage; two different amino acid sequences are read in different frames from the same stretch of DNA. This phenomenon appears contradictory in that the information in the two overlaid amino acid sequences is strongly interdependent, yet each of the two proteins has evolved to its own well-defined function. The contradiction can be resolved by assuming sufficiently large degeneracy of the information contents of amino acid sequences with respect to function. Such a degeneracy is familiar from homologous proteins where a given biological function is implemented by many different amino acid sequences. It is shown that the very existence of viral overlays allows to derive a lower limit for the magnitude of this degeneracy: The degeneracy is equal to, or greater than fourfold; on the average, at each position of the chain a choice of 1 out of 5 or less amino acids, and not a choice of 1 out of 20 is necessary for constructing a protein with a specified function. In addition, the strong dependence of overlay probabilities on chain length allows the definition of a maximal length of overlays; in bacterial viruses overlay regions should be shorter than about 150 residues.