Publication:
Binding energy analysis for wild-type and Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: Quantum chemical calculations based on the ONIOM method

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Issued Date

2005

Resource Type

Article

File Type

application/pdf

ISSN

8873585

DOI

10.1002/prot.20690

Other identifier(s)

2-s2.0-28644442414

Rights Holder(s)

Scopus

Bibliographic Citation

Proteins: Structure, Function and Genetics. Vol 61, No.4 (2005), p.859-869

Suggested Citation

Saen-Oon S., Kuno H., Hannongbua S. Binding energy analysis for wild-type and Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: Quantum chemical calculations based on the ONIOM method. Proteins: Structure, Function and Genetics. Vol 61, No.4 (2005), p.859-869. doi:10.1002/prot.20690 Retrieved from: https://hdl.handle.net/20.500.14740/6042

Title

Binding energy analysis for wild-type and Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: Quantum chemical calculations based on the ONIOM method

Author(s)

Saen-Oon S.
 Kuno H.
 Hannongbua S.

Abstract

Two-layered and three-layered ONIOM calculations were performed to compare the binding energies of 8-Cl TIBO inhibitor when bound into the human immunodeficiency virus reverse transcriptase binding pocket and a Y181C variant. Both consisted of 20 residues within a radius of 15 Å. A combination of different methods [HP2/6-31G(d), B3LYP/6-31G(d,p), and PM3] were performed to take advantage of ONIOM's layering strategy analysis. The obtained results clearly indicate that the Y181C mutation reduces the binding affinity and stability of the inhibitor by approximately 8-9 kcal/mol as obtained from different combined MO:MO methods. Analyses regarding the energetic components of the interaction and deformation energies for 8-Cl TIBO inhibitor upon binding were also examined extensively. Additional calculations involving the interaction energies between 8-Cl TIBO with individual residues surrounding the binding pocket were performed at MP2/6-31G(d,p) and B3LYP/6-31G(d,p) levels of theory to gain more insight into the energetic differences of wild-type and Y181C mutant type at the atomistic level. © 2005 Wiley-Liss, Inc.

Subject(s)

4,5,6,7 tetrahydroimidazo 8 chloro 5 methyl (3 methyl 2 butenyl)imidazo
 RNA directed DNA polymerase
 RNA directed DNA polymerase inhibitor
 Unclassified drug
 Analytic method
 Article
 Binding affinity
 Calculation
 Comparative study
 Complex formation
 Drug binding site
 Drug protein binding
 Energy
 Human immunodeficiency virus 1
 Molecular stability
 Mutation
 Nonhuman
 Priority journal
 Quantum chemistry
 Wild type
 Amino Acid Substitution
 Dimerization
 HIV-1
 Kinetics
 Models, Molecular
 Polymorphism, Single Nucleotide
 Protein Structure, Secondary
 Protein Subunits
 Quantum Theory
 Recombinant Proteins
 Reverse Transcriptase Inhibitors
 RNA-Directed DNA Polymerase
 Thermodynamics
 Human immunodeficiency virus
 Human immunodeficiency virus 1

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URI

https://hdl.handle.net/20.500.14740/6042

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Scopus: Year 1983-2021

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