Analysis of Internal Motion from Molecular Dynamics of Major Urinary Protein I

NOVÁK, Petr and Pavel MACEK. Analysis of Internal Motion from Molecular Dynamics of Major Urinary Protein I. Materials Structure. Praha: The Czech and Slovak Cryst. Assoc., 2004, vol. 11, No 1, p. 51-51. ISSN 1211-5894.

Basic information

Original name

Analysis of Internal Motion from Molecular Dynamics of Major Urinary Protein I

Name in Czech

Analýza vnitřních pohybů z molekulové dynamiky proteinu MUP I

Authors

NOVÁK, Petr (203 Czech Republic, guarantor) and Pavel MACEK (203 Czech Republic)

Edition

Materials Structure, Praha, The Czech and Slovak Cryst. Assoc. 2004, 1211-5894

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Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

RIV identification code

RIV/00216224:14310/04:00011144

Organization unit

Faculty of Science

Keywords in English

molecular dynamics; MUP;

Tags

molecular dynamics, MUP

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Abstract

V originále

Investigation of the protein of mouse urine has shown that it consists predominantly of a group of closely related proteins termed the Major Urinary Proteins (MUPs). These are acidic proteins (pI values from 4.2 to 4.7) with molecular masses of approximately 19 kDa. The MUPs are associated with pheromonally active ligands including relatively tightly bound 2-sec-butyl-4,5-dihydrothiazole. Thus MUPs may serve as a model of proteins binding small, hydrophobic ligands that are known to possess the capability of chemical signaling. Structure of MUP-I was determined crystallographically. The X-ray structures of MUP-I with and without ligand were taken and hydrogens, counter-ions and box of explicit water molecules were added. The system was minimized, heated and equilibrated and then the molecular dynamics was ran. From whole trajectory a 6ns-long part was taken and used for further analysis of internal motions of MUP-I. Correlation functions and frequency dependent order parameters have been calculated.All molecular dynamics was performed with AMBER7 software package.

In Czech

Z trajektorie vzniklé ze simulace molekulové dynamiky proteinu MUP-I byly vypočteny parametry popisující vnitřní pohyby v molekule proteinu.

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Links

LN00A016, research and development project

Name: BIOMOLEKULÁRNÍ CENTRUM Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Center