Studies of N-terminal templates for .alpha.-helix formation. Synthesis and conformational analysis of peptide conjugates of (2S,5S,8S,11S)-1-acetyl-1,4-diaza-3-keto-5-carboxy-10-thiatricyclo[2.8.1.04,8]tridecane (Ac-Hel1-OH)

1991 ◽  
Vol 56 (23) ◽  
pp. 6683-6697 ◽  
Author(s):  
D. S. Kemp ◽  
Timothy P. Curran ◽  
James G. Boyd ◽  
Thomas J. Allen
Keyword(s):  
Conformational Analysis ◽  
Alpha Helix ◽  
Peptide Conjugates ◽  
Helix Formation

ALPHA-HELIX FORMATION IN C-PEPTIDE RNASE-A INVESTIGATED BY PARALLEL TEMPERING SIMULATIONS

2007 ◽  
Vol 18 (01) ◽  
pp. 91-98 ◽  
Author(s):  
GÖKHAN GÖKOĞLU ◽  
TARIK ÇELİK
Keyword(s):  
Energy State ◽  
Minimum Energy ◽  
Alpha Helix ◽  
Salt Bridge ◽  
Rnase A ◽  
Parallel Tempering ◽  
Implicit Solvent ◽  
C Peptide ◽  
Helix Formation ◽  
Α Helix

We have performed parallel tempering simulations of a 13-residue peptide fragment of ribonuclease-A, c-peptide, in implicit solvent with constant dielectric permittivity. This peptide has a strong tendency to form α-helical conformations in solvent as suggested by circular dichroism (CD) and nuclear magnetic resonance (NMR) experiments. Our results demonstrate that 5th and 8–12 residues are in the α-helical region of the Ramachandran map for global minimum energy state in solvent environment. Effects of salt bridge formation on stability of α-helix structure are discussed.

A Model of a Protein $${\alpha}$$ Helix Formation Based on the Two-Particle Model of Motion in the Lennard-Jones Potential

2021 ◽  
Vol 76 (4) ◽  
pp. 226-232
Author(s):  
K. A. Zuev ◽  
N. T. Levashova ◽  
E. V. Malyshko ◽  
A. E. Sidorova ◽  
V. A. Tverdislov
Keyword(s):  
Alpha Helix ◽  
Particle Model ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones ◽  
Helix Formation

The Mechanism of alpha-Helix Formation by Peptides

1992 ◽  
Vol 21 (1) ◽  
pp. 95-118 ◽  
Author(s):  
J. Martin Scholtz ◽  
Robert L. Baldwin
Keyword(s):  
Alpha Helix ◽  
Helix Formation

Epitopes of adhesion-perturbing monoclonal antibodies map within a predicted alpha-helical domain of the integrin beta 1 subunit

1997 ◽  
Vol 110 (20) ◽  
pp. 2619-2628
Author(s):  
D.T. Shih ◽  
D. Boettiger ◽  
C.A. Buck
Keyword(s):  
Ligand Binding ◽  
Critical Role ◽  
Alpha Helix ◽  
Cation Binding ◽  
Affinity Column ◽  
Integrin Subunit ◽  
Amino Acid Residues ◽  
Helix Formation ◽  
Ligand Interactions ◽  
Integrin Ligand

Several recent studies have demonstrated the involvement of various domains of the beta 1 integrin subunit in ligand binding. Thus, specific amino acids have been shown to be important in divalent cation binding, and others have been implicated by peptide crosslinking to play an intimate role in integrin-ligand interactions. Added to these data are previous observations that a group of adhesion-blocking anti-chicken beta 1 antibodies mapped within the first 160 amino acid residues of the subunit. These observations suggested that this region plays a critical role in integrin ligand recognition. In order to further define the domain in which the epitopes for these antibodies are clustered, a series of mouse/chicken chimeric beta 1 constructs were examined for their reactivity with each of these antibodies. Most of the antibodies recognize a region between residues 124 to 160 of the chicken beta 1 subunit. Computer modeling predicted a possible amphipathic alpha-helical configuration for the region between residues 141 to 160. Consistent with this prediction, circular dichroism and NMR analysis revealed a tendency for a synthetic peptide containing these residues to form an alpha-helix. The significance of this structural characteristic was demonstrated by a mutation at residue 149 that disrupted the alpha-helix formation and resulted in a loss of the ability to form heterodimers with alpha subunits, localize to focal contacts, or be transported to the cell surface. The direct involvement of residues 141 to 160 in ligand binding was supported by the ability of a peptide with this sequence to elute integrins from a fibronectin affinity column. Thus, our data suggest that residues 141 to 160 of the integrin beta 1 subunit, when arranged in an alpha-helix configuration, participate in ligand binding.

An Improved Synthesis of a Template for .alpha.-Helix Formation

1995 ◽  
Vol 60 (2) ◽  
pp. 454-457 ◽  
Author(s):  
Kim F. McClure ◽  
Peter Renold ◽  
D. S. Kemp
Keyword(s):  
Alpha Helix ◽  
Helix Formation

scholarly journals Helix-coil transition theories. Are they correct?

1997 ◽  
Vol 44 (3) ◽  
pp. 423-432 ◽  
Author(s):  
A Bierzyński ◽  
K Pawłowski
Keyword(s):  
Water Solution ◽  
Alpha Helix ◽  
Theoretical Description ◽  
Random Coil ◽  
Specific Situation ◽  
Amino Acid Residues ◽  
Helix Formation ◽  
Helix Nucleation ◽  
Propagation Parameters ◽  
Helix Propagation

Principles of contemporary theoretical description of alpha-helix formation by polypeptide chains in water solution are shortly presented and critically discussed. The theory treats the unfolded state of a peptide as "random coil"--an ideal conformation quite distant from reality. We suggest that for this reason the helix propagation parameters of amino-acid residues, determined using series of model peptides with different sequential patterns, are not the same. Interpretation of the so called "nucleation parameter" is erroneous. In fact, it is not determined by the helix nucleation process but rather by a specific situation of residues at the helix N- and C-termini, and it strongly depends on solvation of their NH and CO groups, respectively. Consequently, helical segments with terminal sequences dominated by residues with strongly hydrophobic, bulky side chains can be very unstable. We postulate that an unexpectedly high stability of very short, pre-nucleated helices studied by us arises from a "helix end separation effect": separated helix termini are better solvated than when they overlap each other. Because of this effect, helix initiation may be much more difficult than predicted by the theoretical "helix nucleation parameters".

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