title: Effects of the protonation state of the catalytic residues and ligands upon binding and recognition in targeted proteins of HIV-1 and influenza viruses.
abstract: The determination of the protonation state of the functional groups of ligands, and the amino acid residues with electrically charged side chains (His, Lys, Arg, Asp and Glu) or the nucleotide bases of the nucleic acids that they interact with, is important for ligand binding and recognition, the enzyme activity and reaction mechanism, and protein folding/unfolding and stability. Herein, the effects of different protonation state assignments of the small substrate and inhibitors and the critical residues on the reverse transcriptase and protease of human immunodeficiency virus type 1 (HIV-1) and the M2 proton channel of influenza A virus are reviewed. Theoretical studies on these topics are summarized and compared with the experimental data.
authors.affiliation: Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 44150, Thailand.
authors.forename: Nadtanet
authors.initials: N
authors.lastname: Nunthaboot
authors.forename: Thanyada
authors.initials: T
authors.lastname: Rungrotmongkol
authors.forename: Ornjira
authors.initials: O
authors.lastname: Aruksakunwong
authors.forename: Supot
authors.initials: S
authors.lastname: Hannongbua
mesh_terms: D020134:Catalytic Domain; D016333:HIV Protease / Q000737:chemistry / Q000378:metabolism*; D054303:HIV Reverse Transcriptase / Q000378:metabolism*; D015497:HIV-1 / Q000378:metabolism*; D009980:Influenza A virus / Q000378:metabolism*; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011522:Protons; D014763:Viral Matrix Proteins / Q000737:chemistry / Q000378:metabolism*; D000086082:Viroporin Proteins
chemical_list: D016333:HIV Protease; D054303:HIV Reverse Transcriptase; D008024:Ligands; D011522:Protons; D014763:Viral Matrix Proteins; C488937:M2 protein, Influenza A virus; D000086082:Viroporin Proteins; C514824:reverse transcriptase, Human immunodeficiency virus 1; C514803:p16 protease, Human immunodeficiency virus 1