Mimicry by asx‐ and ST‐turns of the four main types of β‐turn in proteins

Hydrogen‐bonded β‐turns in proteins occur in four categories: type I (the most common), type II, type II', and type I'. Asx‐turns resemble β‐turns, in that both have an NH…OC hydrogen bond forming a ring of 10 atoms. Serine and threonine side chains also commonly form hydrogen‐bonded turns, here called ST‐turns. Asx‐turns and ST‐turns can be categorized into four classes, based on side chain rotamers and the conformation of the central turn residue, which are geometrically equivalent to the four types of β‐turns. We propose asx‐ and ST‐turns be named using the type I, II, I', and II' β‐turn nomenclature. Using this, the frequency of occurrence of both asx‐ and ST‐turns is: type II' > type I > type II > type I', whereas for β‐turns it is type I > type II > type I' > type II'. Almost all type II asx‐turns occur as a recently described three residue feature named an asx‐nest.

[1]  C. Venkatachalam Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units , 1968, Biopolymers.

[2]  H. Scheraga,et al.  Chain reversals in proteins. , 1973, Biochimica et biophysica acta.

[3]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[4]  J. Richardson,et al.  Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase. , 1980, Journal of molecular biology.

[5]  D C Rees,et al.  Refined crystal structure of carboxypeptidase A at 1.54 A resolution. , 1983, Journal of molecular biology.

[6]  E. Baker,et al.  Hydrogen bonding in globular proteins. , 1984, Progress in biophysics and molecular biology.

[7]  J. Thornton,et al.  Analysis and prediction of the different types of β-turn in proteins , 1988 .

[8]  G. Rose,et al.  Helix signals in proteins. , 1988, Science.

[9]  J. Richardson,et al.  Corrections: Amino Acid Preferences for Specific Locations at the Ends of α Helices , 1988 .

[10]  J. Richardson,et al.  Amino acid preferences for specific locations at the ends of alpha helices. , 1988, Science.

[11]  J. Richardson,et al.  Principles and Patterns of Protein Conformation , 1989 .

[12]  J. Thornton,et al.  Beta-turns and their distortions: a proposed new nomenclature. , 1990, Protein engineering.

[13]  J. Thornton,et al.  A revised set of potentials for β‐turn formation in proteins , 1994 .

[14]  P Argos,et al.  The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins. , 1994, Journal of molecular biology.

[15]  J. Thornton,et al.  PROMOTIF—A program to identify and analyze structural motifs in proteins , 1996, Protein science : a publication of the Protein Society.

[16]  S. Rowsell Crystal structure of carboxypeptidase G←2. , 1996 .

[17]  J. Thornton,et al.  Structures of N‐termini of helices in proteins , 1997, Protein science : a publication of the Protein Society.

[18]  R. Aurora,et al.  Helix capping , 1998, Protein science : a publication of the Protein Society.

[19]  J. Chandrasekhar,et al.  Conformational interconversions in peptide beta-turns: analysis of turns in proteins and computational estimates of barriers. , 1998, Journal of molecular biology.

[20]  C. Ramakrishnan,et al.  Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures. , 1999, Protein engineering.

[21]  H. Qian,et al.  Hydrogen bonds between short polar side chains and peptide backbone: Prevalence in proteins and effects on helix‐forming propensities , 1999, Proteins.

[22]  E. Milner-White,et al.  A natural grouping of motifs with an aspartate or asparagine residue forming two hydrogen bonds to residues ahead in sequence: their occurrence at alpha-helical N termini and in other situations. , 1999, Journal of molecular biology.

[23]  M. Zalis,et al.  Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. , 1999, Journal of molecular biology.

[24]  J. Richardson,et al.  Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. , 1999, Journal of molecular biology.

[25]  E J Milner-White,et al.  A recurring two-hydrogen-bond motif incorporating a serine or threonine residue is found both at alpha-helical N termini and in other situations. , 1999, Journal of molecular biology.

[26]  J. Richardson,et al.  The penultimate rotamer library , 2000, Proteins.

[27]  C. Ramakrishnan,et al.  Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures. , 2000, Protein engineering.

[28]  N. Inestrosa,et al.  Molecular modeling of the collagen-like tail of asymmetric acetylcholinesterase. , 2000, Protein engineering.

[29]  D. Pal,et al.  The interrelationships of side-chain and main-chain conformations in proteins. , 2001, Progress in biophysics and molecular biology.

[30]  J. Watson,et al.  The conformations of polypeptide chains where the main-chain parts of successive residues are enantiomeric. Their occurrence in cation and anion-binding regions of proteins. , 2002, Journal of molecular biology.

[31]  J. Watson,et al.  A novel main-chain anion-binding site in proteins: the nest. A particular combination of phi,psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions. , 2002, Journal of molecular biology.

[32]  P. Chakrabarti,et al.  Sequence and structure patterns in proteins from an analysis of the shortest helices: implications for helix nucleation. , 2003, Journal of molecular biology.

[33]  Ian W. Davis,et al.  Structure validation by Cα geometry: ϕ,ψ and Cβ deviation , 2003, Proteins.