Effects of Side-Chain Charges on α-Helix Stability in C-Peptide of Ribonuclease A Studied by Multicanonical Algorithm

1999 ◽  
Vol 103 (9) ◽  
pp. 1595-1604 ◽  
Author(s):  
Ulrich H. E. Hansmann ◽  
Yuko Okamoto
Keyword(s):  
Ribonuclease A ◽  
Side Chain ◽  
C Peptide ◽  
Helix Stability ◽  
Α Helix

The Glu 2− ⋯ Arg 10+ side-chain interaction in the C-peptide helix of ribonuclease A

1990 ◽  
Vol 37 (1-3) ◽  
pp. 107-119 ◽  
Author(s):  
Robert Fairman ◽  
Kevin R. Shoemaker ◽  
Eunice J. York ◽  
John M. Stewart ◽  
Robert L. Baldwin
Keyword(s):  
Ribonuclease A ◽  
Side Chain ◽  
C Peptide ◽  
Chain Interaction

scholarly journals Prediction of α-Helix Folding of Isolated C-Peptide of Ribonuclease A by Monte Carlo Simulated Annealing

1991 ◽  
Vol 20 (2) ◽  
pp. 213-216 ◽  
Author(s):  
Hikaru Kawai ◽  
Yuko Okamoto ◽  
Masataka Fukugita ◽  
Takashi Nakazawa ◽  
Takeshi Kikuchi
Keyword(s):  
Monte Carlo ◽  
Simulated Annealing ◽  
Ribonuclease A ◽  
C Peptide ◽  
Monte Carlo Simulated Annealing ◽  
Α Helix

α-Helix folding by Monte Carlo simulated annealing in isolated C-peptide of ribonuclease A

1991 ◽  
Vol 4 (6) ◽  
pp. 639-647 ◽  
Author(s):  
Yuko Okamoto ◽  
Masataka Fukugita ◽  
Takashi Nakazawa ◽  
Hikaru Kawai
Keyword(s):  
Monte Carlo ◽  
Simulated Annealing ◽  
Ribonuclease A ◽  
C Peptide ◽  
Monte Carlo Simulated Annealing ◽  
Α Helix

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.

Stabilising Non-Polar/Polar Side Chain Interactions in the α-Helix

2000 ◽  
Vol 28 (3) ◽  
pp. A72-A72
Author(s):  
Charles D. Andrew ◽  
Simon Penel ◽  
Gareth R. Jones ◽  
Andrew J. Doig
Keyword(s):  
Side Chain ◽  
Α Helix

Structure, stability and folding of the α-helix

2001 ◽  
Vol 68 ◽  
pp. 95-110 ◽  
Author(s):  
Andrew J. Doig ◽  
Charles D. Andrew ◽  
Duncan A. E. Cochran ◽  
Eleri Hughes ◽  
Simon Penel ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrophobic Interactions ◽  
Data Bank ◽  
Site Directed Mutagenesis ◽  
Model Systems ◽  
Side Chain ◽  
Structure Stability ◽  
Helical Peptides ◽  
Vast Number ◽  
Α Helix

Pauling first described the α-helix nearly 50 years ago, yet new features of its structure continue to be discovered, using peptide model systems, site-directed mutagenesis, advances in theory, the expansion of the Protein Data Bank and new experimental techniques. Helical peptides in solution form a vast number of structures, including fully helical, fully coiled and partly helical. To interpret peptide results quantitatively it is essential to use a helix/coil model that includes the stabilities of all these conformations. Our models now include terms for helix interiors, capping, side-chain interactions, N-termini and 310-helices. The first three amino acids in a helix (N1, N2 and N3) and the preceding N-cap are unique, as their amide NH groups do not participate in backbone hydrogen bonding. We surveyed their structures in proteins and measured their amino acid preferences. The results are predominantly rationalized by hydrogen bonding to the free NH groups. Stabilizing side-chain-side-chain energies, including hydrophobic interactions, hydrogen bonding and polar/non-polar interactions, were measured accurately in helical peptides. Helices in proteins show a preference for having approximately an integral number of turns so that their N- and C-caps lie on the same side. There are also strong periodic trends in the likelihood of terminating a helix with a Schellman or αL C-cap motif. The kinetics of α-helix folding have been studied with stopped-flow deep ultraviolet circular dichroism using synchrotron radiation as the light source; this gives a far superior signal-to-noise ratio than a conventional instrument. We find that poly(Glu), poly(Lys) and alanine-based peptides fold in milliseconds, with longer peptides showing a transient overshoot in helix content.

β-Hairpin Crowding Agents Affect α-Helix Stability in Crowded Environments

2016 ◽  
Vol 120 (4) ◽  
pp. 650-659 ◽  
Author(s):  
Bryanne Macdonald ◽  
Shannon McCarley ◽  
Sundus Noeen ◽  
Alan E. van Giessen
Keyword(s):  
Helix Stability ◽  
Α Helix ◽  
Crowded Environments

scholarly journals LK peptide side chain dynamics at interfaces are independent of secondary structure

2017 ◽  
Vol 19 (42) ◽  
pp. 28507-28511 ◽  
Author(s):  
Michael A. Donovan ◽  
Helmut Lutz ◽  
Yeneneh Y. Yimer ◽  
Jim Pfaendtner ◽  
Mischa Bonn ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Real Time ◽  
Surface Interactions ◽  
Side Chain ◽  
Chain Dynamics ◽  
Air Interface ◽  
Time Observation ◽  
Α Helix ◽  
Side Chain Dynamics ◽  
Real Time Observation

Real-time observation of the ultrafast motions of leucine side chains within model peptides at the water–air interface with representative folds – α-helix, 310-helix, β-strand – show that interfacial dynamics are mostly determined by surface interactions.

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