Searching for the simplest structural units to describe the three-dimensional structure of proteins

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Abstract

Ab initio computations have been carried out during the past several years on diamides of single amino acids (HCO-NHCHR-CONH2 where R=H (glycine), -CH3 (alanine), -CH(CH3)2 (valine) and -CH2OH (serine)) exploring all possible backbone and side chain conformations. Selected conformations were studied in our laboratory on threonine (R=CH(CH3)OH), cystein (R=CH2-SH) and phenylalanine (R=CH2-C5H6) diamides. Tri-, tetra-, penta-, hexa- and hepta-amide systems of poly-L-alanine (H-(CONH-CHCH3-CONH)n-H 2 ≤n ≤ 6) were also investigated at selected backbone conformations. All these studies confirmed the results of multidimensional conformation analyses: the ith amino acid residue in a polypeptide has a maximum of nine (9) discrete backbone conformations. These structures correspond to nine conformational centres on the 2D-Ramachandran map. On the basis of this finding, it can be shown that the folded secondary structure of any protein with known internal coordinates, can be described in terms of these nine discrete conformation types.

Original languageEnglish
Pages (from-to)127-168
Number of pages42
JournalInternational Reviews in Physical Chemistry
Volume14
Issue number1
Publication statusPublished - 1995

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alanine
amides
amino acids
Conformations
methylidyne
proteins
phenylalanine
polypeptides
glycine
Diamide
Proteins
Amides
Amino Acids
Valine
Threonine
Phenylalanine
Alanine
Glycine
Serine
Peptides

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

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title = "Searching for the simplest structural units to describe the three-dimensional structure of proteins",
abstract = "Ab initio computations have been carried out during the past several years on diamides of single amino acids (HCO-NHCHR-CONH2 where R=H (glycine), -CH3 (alanine), -CH(CH3)2 (valine) and -CH2OH (serine)) exploring all possible backbone and side chain conformations. Selected conformations were studied in our laboratory on threonine (R=CH(CH3)OH), cystein (R=CH2-SH) and phenylalanine (R=CH2-C5H6) diamides. Tri-, tetra-, penta-, hexa- and hepta-amide systems of poly-L-alanine (H-(CONH-CHCH3-CONH)n-H 2 ≤n ≤ 6) were also investigated at selected backbone conformations. All these studies confirmed the results of multidimensional conformation analyses: the ith amino acid residue in a polypeptide has a maximum of nine (9) discrete backbone conformations. These structures correspond to nine conformational centres on the 2D-Ramachandran map. On the basis of this finding, it can be shown that the folded secondary structure of any protein with known internal coordinates, can be described in terms of these nine discrete conformation types.",
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AU - Csizmadia, I.

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AB - Ab initio computations have been carried out during the past several years on diamides of single amino acids (HCO-NHCHR-CONH2 where R=H (glycine), -CH3 (alanine), -CH(CH3)2 (valine) and -CH2OH (serine)) exploring all possible backbone and side chain conformations. Selected conformations were studied in our laboratory on threonine (R=CH(CH3)OH), cystein (R=CH2-SH) and phenylalanine (R=CH2-C5H6) diamides. Tri-, tetra-, penta-, hexa- and hepta-amide systems of poly-L-alanine (H-(CONH-CHCH3-CONH)n-H 2 ≤n ≤ 6) were also investigated at selected backbone conformations. All these studies confirmed the results of multidimensional conformation analyses: the ith amino acid residue in a polypeptide has a maximum of nine (9) discrete backbone conformations. These structures correspond to nine conformational centres on the 2D-Ramachandran map. On the basis of this finding, it can be shown that the folded secondary structure of any protein with known internal coordinates, can be described in terms of these nine discrete conformation types.

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