Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody fab fragment at 2.8 Å resolution

1998 ◽  
Vol 284 (4) ◽  
pp. 1095-1111 ◽  
Author(s):  
Jianping Ding ◽  
Kalyan Das ◽  
Yu Hsiou ◽  
Stefan G Sarafianos ◽  
Arthur D Clark ◽  
...  
Keyword(s):  
Active Site ◽  
Fab Fragment ◽  
Double Stranded Dna ◽  
Functional Implications ◽  
Dna Template ◽  
Active Site Region ◽  
Hiv 1

scholarly journals Activity of linked HIV-1 proteinase dimers containing mutations in the active site region

1996 ◽  
Vol 9 (11) ◽  
pp. 997-1003 ◽  
Author(s):  
Péter Bagossi ◽  
Yin-Shyun E. Cheng ◽  
Stephen Oroszlan ◽  
József Tözsér
Keyword(s):  
Active Site ◽  
Active Site Region ◽  
Hiv 1

MECHANISTIC STUDY OF HIV-1 REVERSE TRANSCRIPTASE AT THE ACTIVE SITE BASED ON QM/MM METHOD

2004 ◽  
Vol 03 (04) ◽  
pp. 491-500 ◽  
Author(s):  
THANYADA RUNGROTMONGKOL ◽  
SUPA HANNONGBUA ◽  
ADRIAN MULHOLLAND
Keyword(s):  
Reverse Transcriptase ◽  
Active Site ◽  
Complex Structure ◽  
Genetic Material ◽  
Mechanistic Study ◽  
Energy Profiles ◽  
Double Stranded Dna ◽  
Dynamics Simulations ◽  
Hiv 1

HIV-1 RT catalyses the reverse transcription of viral genetic material (RNA) into double-stranded DNA, and is an important target of antiviral therapy in the treatment of AIDS. Better understanding of the structure, mechanism and functional role of residues involved in the resistance of HIV-1 RT against nucleoside-analog drugs may assist in the development of improved inhibitors, and also in understanding the effects of genetic variation on RT specificity and activity. In this study, firstly, molecular dynamics simulations (with CHARMM27) have been used to investigate binding interactions at the active site and the conformational behavior of the enzyme, then, mechanisms of deprotonation and DNA polymerization reactions have been modelled by the QM/MM method. A combined quantum mechanical and molecular mechanical (QM/MM) method (AM1/CHARMM) has been used to study the triphosphate substrate and the active site of HIV-1 reverse transcriptase complex structure, a virally-encoded enzyme. Free energy profiles for the reaction are also calculated. The obtained results provide important insight into the mechanistic activity of HIV-1 RT.

scholarly journals Selective chemical autoligation on a double-stranded DNA template

1994 ◽  
Vol 22 (23) ◽  
pp. 5076-5078 ◽  
Author(s):  
Mathias K. Herrlein ◽  
Robert L. Letsinger
Keyword(s):  
Double Stranded Dna ◽  
Selective Chemical ◽  
Dna Template

scholarly journals Mechanism of HIV-1 NC Protein-Induced Condensation of Double Stranded DNA as a Model for DNA Compaction during Reverse Transcription

2021 ◽  
Vol 120 (3) ◽  
pp. 206a
Author(s):  
Helena Gien ◽  
Michael Morse ◽  
Jonathan Kitzrow ◽  
Ioulia F. Rouzina ◽  
Karin Musier-Forsyth ◽  
...  
Keyword(s):  
Reverse Transcription ◽  
Dna Compaction ◽  
Double Stranded Dna ◽  
Hiv 1
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