Thermal Stability of the Secondary Structure of Poly(α,L-glutamate) in Self-Assembled Complexes as Studied by Molecular Dynamics in Chloroform Solution

Journal of the American Chemical Society

Volumn 126, Issue 3, 2004, Pages 704-705

  Zanuy, David ^a   Casanovas, Jordi ^b   Alemán, Carlos ^c  

^a NATIONAL CANCER INSTITUTE   (United States)

^b UNIVERSITY OF LLEIDA   (Spain)

^c UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROFORM; GLUTAMIC ACID DERIVATIVE; POLYPEPTIDE;

ARTICLE; CHEMICAL INTERACTION; CIRCULAR DICHROISM; CONFORMATION; HYDROGEN BOND; INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; PROTEIN SECONDARY STRUCTURE; STOICHIOMETRY; TEMPERATURE DEPENDENCE; THERMOSTABILITY; X RAY DIFFRACTION;

CHLOROFORM; HEAT; POLYGLUTAMIC ACID; PROTEIN STRUCTURE, SECONDARY; QUATERNARY AMMONIUM COMPOUNDS; SOLUTIONS; SURFACE-ACTIVE AGENTS; THERMODYNAMICS;

EID: 1642535362     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja036803e     Document Type: Article

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7. 3), which were previously equilibrated in a cubic box. The molecular system was constructed by centering the complex in the solvent box and deleting the overlapping solvent molecules. Simulations at 300, 350, and 400 K were of constant pressure and temperature (NPT) type. In these cases, the system was brought to the desired temperature by in ps of constant volume and temperature (NVT) MD, where in ranges from 750 to 1100, with the hydrogen-bonding distances of the α-helix constrained at 2 Å. After this, the system was equilibrated at P = 1 atm by performing 100 ps of NPT MD, in which no constraint was applied. The resulting structures were used as starting points of NPT MD simulations, each one consisting of a total of 6 ns. For the simulations at 450 and 500 K, we used as a starting point the complex equilibrated at 400 K, the temperature being gradually increased along 100-250 ps of NVT MD. Then, the complexes were equilibrated for an additional 200 ps using NPT MD. Two independent systems were prepared at each temperature, which differed only in the length of the trajectory used for the last heating. Accordingly, our production runs at these temperatures consisted of four independent NVT MD, which were 6-ns long. However, one of the simulations at 500 K was enlarged to 12 ns to improve the sampling. To estimate the melting temperature, additional NVT simulations were performed using the same protocol at 600, 700, and 800 K, which were as much 4-ns long. Parameter settings not commented on here and the force field were as in ref 4a. MD simulations (6-ns long) were also done for a PALG helix with dodecyl chains covalently linked to the ester groups (450 K) and for helical polyalanine (300, 350, and 400 K), 15 residues being considered in both cases. The heating and the equilibration protocols were similar to those displayed above for the complex. Forcefield parameters for the PALG derivative were derived using the same procedure as in ref 4a, while parameters for polyalanine were directly taken from Amber libraries.
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