scholarly journals Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin

BIOPHYSICS ◽  
2010 ◽  
Vol 6 ◽  
pp. 67-78 ◽  
Author(s):  
Hiroshi C. Watanabe ◽  
Yoshiharu Mori ◽  
Takashi Tada ◽  
Shozo Yokoyama ◽  
Takahisa Yamato
Keyword(s):  
Amino Acid ◽  
Molecular Mechanism ◽  
Long Range ◽  
Amino Acid Residues ◽  
Color Tuning ◽  
Multiple Amino Acid

CDDO-imidazolide Targets Multiple Amino Acid Residues on the Nrf2 Adaptor, Keap1

2020 ◽  
Vol 63 (17) ◽  
pp. 9965-9976 ◽  
Author(s):  
Xiaoli Meng ◽  
James C. Waddington ◽  
Arun Tailor ◽  
Adam Lister ◽  
Jane Hamlett ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Residues ◽  
Multiple Amino Acid

scholarly journals Molecular Mechanism of DAPD/DXG against Zidovudine- and Lamivudine- Drug Resistant Mutants: A Molecular Modelling Approach

2002 ◽  
Vol 13 (2) ◽  
pp. 115-128 ◽  
Author(s):  
Youhoon Chong ◽  
Katyna Borroto-Esoda ◽  
Phillip A Furman ◽  
Raymond F Schinazi ◽  
Chung K Chu
Keyword(s):  
Drug Resistance ◽  
Amino Acid ◽  
Antiviral Activity ◽  
Molecular Mechanism ◽  
Binding Affinity ◽  
Molecular Modelling ◽  
Enzyme Inhibitor ◽  
Drug Resistant ◽  
Amino Acid Residues ◽  
Resistant Mutants

In order to understand molecular mechanism of antiviral drug resistance of HIV-1 reverse transcriptase (RT) as well as potent antiviral activity of 2,6-diaminopurine dioxolane (DAPD) [prodrug of (–)-β-D-dioxolane guanine (DXG)] against drug-resistant RTs, molecular modelling studies of three structurally distinct nucleoside RT inhibitor (NRTI)-triphosphates (TP) [zidovudine (AZT)-TP, lamivudine (3TC)-TP and DXG-TP] complexed with the wild-type (WT) and mutated RT were conducted. The computational analyses indicated that the antiviral activity and the calculated relative binding energy of the RT inhibitor triphosphates can be correlated, and the minimized structures gave information on the molecular mechanism of drug resistance conferred by mutations. The interactions between the NRTI-TP and adjacent amino acid residues (Lys65, Lys70, Arg72, Tyr115 and/or Gln151) played important roles in stabilizing the enzyme—inhibitor complex. Particularly, Arg72 was found to stabilize the dioxolane and oxathiolane sugar moiety through hydrogen bonding, which was responsible for favourable binding affinity of DXG-TP to AZT- as well as 3TC-resistant mutants. The conformational changes in these amino acid residues caused by mutation always affected the changes in the tertiary structures of enzyme-inhibitor complexes through either closing or opening the gap between the fingers and palm domains. The enzyme-inhibitor complexes with good binding affinity showed tight binding modes by closing the gap between the two domains, whereas weak inhibitors gave open and loose complexes.

scholarly journals An Evolutionary Perspective of the Lipocalin Protein Family

2021 ◽  
Vol 12 ◽  
Author(s):  
Sergio Diez-Hermano ◽  
Maria D. Ganfornina ◽  
Arne Skerra ◽  
Gabriel Gutiérrez ◽  
Diego Sanchez
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Family ◽  
Gene Duplications ◽  
Amino Acid Residues ◽  
Sequence Alignments ◽  
New Members ◽  
Multiple Amino Acid ◽  
Sequence Similarities ◽  
Tandem Duplications

The protein family of Lipocalins is ubiquitously present throughout the tree of life, with the exception of the phylum Archaea. Phylogenetic relationships of chordate Lipocalins have been proposed in the past based on protein sequence similarities, but their highly divergent primary structures and a shortage of experimental annotations in genome projects have precluded a well-supported hypothesis for their evolution. In this work we propose a novel topology for the phylogenetic tree of chordate Lipocalins, inferred from multiple amino acid sequence alignments. Sixteen jawed vertebrates with fair coverage by genomic sequencing were compared. The selected species span an evolutionary range of ∼400 million years, allowing for a balanced representation of all major vertebrate clades. A consensus phylogenetic tree is proposed following a comparison of sequence-based maximum-likelihood trees and protein structure dendrograms. This new phylogeny suggests an APOD-like common ancestor in early chordates, which gave rise, via whole-genome or tandem duplications, to the six Lipocalins currently present in fish (APOD, RBP4, PTGDS, AMBP, C8G, and APOM). Further gene duplications of APOM and PTGDS resulted in the altogether 15 Lipocalins found in contemporary mammals. Insights into the functional impact of relevant amino acid residues in early diverging Lipocalins are also discussed. These results should foster the experimental exploration of novel functions alongside the identification of new members of the Lipocalin family.

Sign in / Sign up

Export Citation Format

Share Document