Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study

FADRNÁ, Eva, Klára HLADEČKOVÁ a Jaroslav KOČA. Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study. Journal of Biomolecular Structure and Dynamics. USA: Adenine Press, 2005, roč. 23, č. 2, s. 151-162. ISSN 0739-1102.

Základní údaje

• Originální název: Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study
• Název česky: Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study
• Autoři: FADRNÁ, Eva (203 Česká republika, garant), Klára HLADEČKOVÁ (203 Česká republika) a Jaroslav KOČA (203 Česká republika).
• Vydání: Journal of Biomolecular Structure and Dynamics, USA, Adenine Press, 2005, 0739-1102.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Článek v odborném periodiku
• Obor: 10403 Physical chemistry
• Stát vydavatele: Spojené státy
• Utajení: není předmětem státního či obchodního tajemství
• WWW: URL
• Impakt faktor: Impact factor: 1.430
• Kód RIV: RIV/00216224:14310/05:00014160
• Organizační jednotka: Přírodovědecká fakulta
• UT WoS: 000232038800005
• Klíčová slova anglicky: Molecular dynamics; electrostatic interactions; endothelin-1
• Štítky: electrostatic interactions, Endothelin-1, molecular dynamics

Anotace

An extensive conformational search in explicit solvent was performed in order to compare the influence of different long-range electrostatic interaction treatments in molecular dynamics. The short peptide endothelin-1 was selected as the subject of molecular dynamics studies that started from both X-ray and NMR obtained structures. Electrostatic interactions were treated using two of the most common methods -- residue-based cutoff and particle mesh Ewald (PME). Analyses of free energy calculations (MM-PBSA method used), secondary structure elements and hydrogen bonds were performed, and there suggested that there is no unambiguous conclusion about which of the two methods of long-range electrostatics treatment should be used in MD simulations in this case. The most reliable data was provided by a trajectory that started with the NMR structure and used the cutoff method to treat electrostatic interactions. This leads to a recommendation that the choice of electrostatics treatment should be made carefully and not automatically by choosing the PME method simply because it is the most widely used.

Anotace česky

An extensive conformational search in explicit solvent was performed in order to compare the influence of different long-range electrostatic interaction treatments in molecular dynamics. The short peptide endothelin-1 was selected as the subject of molecular dynamics studies that started from both X-ray and NMR obtained structures. Electrostatic interactions were treated using two of the most common methods -- residue-based cutoff and particle mesh Ewald (PME). Analyses of free energy calculations (MM-PBSA method used), secondary structure elements and hydrogen bonds were performed, and there suggested that there is no unambiguous conclusion about which of the two methods of long-range electrostatics treatment should be used in MD simulations in this case. The most reliable data was provided by a trajectory that started with the NMR structure and used the cutoff method to treat electrostatic interactions. This leads to a recommendation that the choice of electrostatics treatment should be made carefully and not automatically by choosing the PME method simply because it is the most widely used.

Návaznosti

• MSM0021622413, záměr: Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím