HELANAL: A Program to Characterize Helix Geometry in Proteins

Abstract A detailed analysis of structural and position dependent characteristic features of helices will give a better understanding of the secondary structure formation in globular proteins. Here we describe an algorithm that quantifies the geometry of helices in proteins on the basis of their Cα atoms alone. The Fortran program HELANAL can extract the helices from the PDB files and then characterises the overall geometry of each helix as being linear, curved or kinked, in terms of its local structural features, viz. local helical twist and rise, virtual torsion angle, local helix origins and bending angles between successive local helix axes. Even helices with large radius of curvature are unambiguously identified as being linear or curved. The program can also be used to differentiate a kinked helix and other motifs, such as helix-loop-helix or a helix-turn-helix (with a single residue linker) with the help of local bending angles. In addition to these, the program can also be used to characterise the helix start and end as well as other types of secondary structures.

[1]  L. Pauling,et al.  The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. , 1951, Proceedings of the National Academy of Sciences of the United States of America.

[2]  J. Kendrew,et al.  A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis , 1958, Nature.

[3]  H. Sugeta,et al.  General method for calculating helical parameters of polymer chains from bond lengths, bond angles, and internal‐rotation angles , 1967 .

[4]  G. N. Ramachandran,et al.  Conformation of polypeptides and proteins. , 1968, Advances in protein chemistry.

[5]  D. Parry,et al.  Interchain packing energies of multistranded α‐helical ropes , 1969 .

[6]  K. B. Ward,et al.  The structures of lamprey and bloodworm hemoglobins in relation to their evolution and function. , 1972, Cold Spring Harbor symposia on quantitative biology.

[7]  M. Levitt,et al.  Automatic identification of secondary structure in globular proteins. , 1977, Journal of molecular biology.

[8]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[9]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[10]  Nivedita Borkakoti,et al.  Solvent-induced distortions and the curvature of α-helices , 1983, Nature.

[11]  D. Rees,et al.  Peptide‐bond distortions and the curvature of α‐helices , 1986 .

[12]  J. Thornton,et al.  Helix geometry in proteins. , 1988, Journal of molecular biology.

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

[14]  F. Richards,et al.  Identification of structural motifs from protein coordinate data: Secondary structure and first‐level supersecondary structure * , 1988, Proteins.

[15]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[16]  P. S. Kim,et al.  X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. , 1991, Science.

[17]  Roderick E. Hubbard,et al.  Analysis of Cα geometry in protein structures , 1994 .

[18]  U. Hobohm,et al.  Enlarged representative set of protein structures , 1994, Protein science : a publication of the Protein Society.

[19]  S. Kumar,et al.  Structural and sequence characteristics of long alpha helices in globular proteins. , 1996, Biophysical journal.

[20]  J. Thornton,et al.  Deviations from planarity of the peptide bond in peptides and proteins. , 1996, Journal of molecular biology.

[21]  Sandeep Kumar,et al.  Dissecting α‐helices: Position‐specific analysis of α‐helices in globular proteins , 1998, Proteins.

[22]  Manju Bansal,et al.  Geometrical and Sequence Characteristics of α-Helices in Globular Proteins , 1998 .