Molecular dynamics simulations on HIV-1 Tat.
Molecular dynamics simulations are used to investigate dynamics and intramolecular interactions of the HIV-1 transactivator (Tat) in aqueous solution. The calculations are based on the AMBER force field with particle mesh Ewald treatment for long-range electrostatics. The Tat structure exhibits a large flexibility, consistent with its absence of secondary structure elements. From an analysis of the correlation matrix and of electrostatic interactions we suggest that segments expressed by the two exons (amino acids 1-72 and 73-86, respectively) exhibit rather separated dynamic and energetic properties. We also identify intramolecular interactions of importance for structure stabilization. In particular, significant electrostatic interactions are recognized between the N-terminus and the basic domain of the protein, consistent with site-directed mutagenesis performed in this work.
Pantano
Sergio
S
International School for Advanced Studies (ISAS) and INFM, DEMOCRITOS Modeling Center for Research in Atomistic Simulation, Via Beirut 2-4, 34014, Trieste, Italy.
Tyagi
Mudit
M
Giacca
Mauro
M
Carloni
Paolo
P
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D001665:Binding Sites; D003198:Computer Simulation; D015696:Gene Products, tat / Q000737:chemistry*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009038:Motion; D016297:Mutagenesis, Site-Directed; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D055672:Static Electricity; D013329:Structure-Activity Relationship; D014867:Water / Q000737:chemistry
D015696:Gene Products, tat; D014867:Water