Helix propagation in trifluoroethanol solutions

Biopolymers ◽  
1992 ◽  
Vol 32 (12) ◽  
pp. 1695-1702 ◽  
Author(s):  
Richard W. Storrs ◽  
Dagmar Truckses ◽  
David E. Wemmer
Keyword(s):  
Helix Propagation

scholarly journals Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol

1996 ◽  
Vol 5 (12) ◽  
pp. 2623-2637 ◽  
Author(s):  
Carol A. Rohl ◽  
Avijit Chakrabartty ◽  
Robert L. Baldwin
Keyword(s):  
Amino Acids ◽  
Volume Percent ◽  
Helix Propagation

Solitary waves of α-helix propagation in media with arbitrary inhomogeneities

2013 ◽  
Vol 86 (5) ◽  
Author(s):  
Alain Mvogo ◽  
Germain Hubert Ben-Bolie ◽  
Timoléon Crépin Kofané
Keyword(s):  
Solitary Waves ◽  
Helix Propagation ◽  
Α Helix

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".

scholarly journals Effects of side chains in helix nucleation differ from helix propagation

2014 ◽  
Vol 111 (18) ◽  
pp. 6636-6641 ◽  
Author(s):  
S. E. Miller ◽  
A. M. Watkins ◽  
N. R. Kallenbach ◽  
P. S. Arora
Keyword(s):  
Side Chains ◽  
Helix Nucleation ◽  
Helix Propagation

Experimental Investigation of Initial Steps of Helix Propagation in Model Peptides†

Biochemistry ◽  
2003 ◽  
Vol 42 (22) ◽  
pp. 6840-6847 ◽  
Author(s):  
Grażyna Goch ◽  
Maciej Maciejczyk ◽  
Marta Oleszczuk ◽  
Damian Stachowiak ◽  
Joanna Malicka ◽  
...  
Keyword(s):  
Experimental Investigation ◽  
Helix Propagation ◽  
Model Peptides

scholarly journals Free energy of helix propagation in short polyalanine chains determined from peptide growth simulations of La3+-binding model peptides. Comparison with experimental data.

2005 ◽  
Vol 53 (1) ◽  
pp. 121-129
Author(s):  
Maciej Maciejczyk ◽  
Jan Hermans ◽  
Andrzej Bierzyński
Keyword(s):  
Experimental Data ◽  
Alpha Helix ◽  
Md Simulations ◽  
Simulation Method ◽  
Conformational Transitions ◽  
Peptide Backbone ◽  
Binding Model ◽  
Peptide System ◽  
Helix Propagation ◽  
Comparison With Experimental Data

Molecular dynamics (MD) is, at present, a unique tool making it possible to study, at the atomic level, conformational transitions in peptides and proteins. Nevertheless, because MD calculations are always based on a more or less approximate physical model, using a set of approximate parameters, their reliability must be tested by comparison with experimental data. Unfortunately, it is very difficult to find a peptide system in which conformational transitions can be studied both experimentally and using MD simulations so that a direct comparison of the results obtained in both ways could be made. Such a system, containing a rigid alpha-helix nucleus stabilized by La(3+) coordination to a 12-residue sequence taken from an EF-hand protein has recently been used to determine experimentally the helix propagation parameters in very short polyalanine segments (Goch et al. (2003) Biochemistry 42: 6840-6847). The same parameters were calculated here for the same peptide system using the peptide growth simulation method with, alternatively, charmm 22 and cedar potential energy functions. The calculated free energies of the helix-coil transition are about two times too large for cedar and even three times too large for charmm 22, as compared with the experimental values. We suggest that these discrepancies have their origin in the incorrect representation of unfolded peptide backbone in solution by the molecular mechanics force fields.

A Microscopic View of Helix Propagation: N and C-terminal Helix Growth in Alanine Helices

1996 ◽  
Vol 259 (3) ◽  
pp. 560-572 ◽  
Author(s):  
William S. Young ◽  
Charles L. Brooks III
Keyword(s):  
Helix Propagation
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