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Lakshmi SA, Shafreen RB, Priyanga A, Shiburaj S, Pandian SK. A highly divergent α-amylase from Streptomyces spp.: An evolutionary perspective. Int J Biol Macromol 2020; 163:2415-2428. [PMID: 32961188 DOI: 10.1016/j.ijbiomac.2020.09.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/01/2020] [Accepted: 09/15/2020] [Indexed: 11/18/2022]
Abstract
The present study deals with the genetic changes observed in the protein sequence of an α-amylase from Streptomyces spp. and its structural homologs from Pseudoalteromonas haloplanktis, invertebrates and mammals. The structural homologs are renowned for their important features such as chloride binding triad and a serine-protease like catalytic triad (a triad which is reported to be strictly conserved in all chloride-dependent α-amylases). These conserved regions are essential for allosteric activation of enzyme and conformational stability, respectively. An evaluation of these distinctive features in Streptomyces α-amylases revealed the role of mutations in conserved regions and evolution of chloride-independent α-amylases in Streptomyces spp. Besides, the study also discovers a highly divergent α-amylase from Streptomyces spp. which varies greatly even within the homologs of the same genus. Another very important feature is the number of disulfide bridges in which the structural homologs own eight Cys residues to form four disulfide bridges whereas Streptomyces α-amylases possess only seven Cys to form three disulfide bridges. The study also highlights the unique evolution of carbohydrate binding module 20 domain (CBM20 also known as raw starch binding domain or E domain) in Streptomyces α-amylases which is completely absent in α-amylases of other structural homologs.
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Affiliation(s)
- Selvaraj Alagu Lakshmi
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630003, Tamil Nadu, India
| | | | - Appasamy Priyanga
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630003, Tamil Nadu, India
| | - Sugathan Shiburaj
- Division of Microbiology, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Palode, Thiruvananthapuram, Kerala 695562, India; Department of Botany, University of Kerala, Kariavattom, Thiruvananthapuram, Kerala 695581, India
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Cook NJ, Li W, Berta D, Badaoui M, Ballandras-Colas A, Nans A, Kotecha A, Rosta E, Engelman AN, Cherepanov P. Structural basis of second-generation HIV integrase inhibitor action and viral resistance. Science 2020; 367:806-810. [PMID: 32001525 DOI: 10.1126/science.aay4919] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 01/15/2020] [Indexed: 11/02/2022]
Abstract
Although second-generation HIV integrase strand-transfer inhibitors (INSTIs) are prescribed throughout the world, the mechanistic basis for the superiority of these drugs is poorly understood. We used single-particle cryo-electron microscopy to visualize the mode of action of the advanced INSTIs dolutegravir and bictegravir at near-atomic resolution. Glutamine-148→histidine (Q148H) and glycine-140→serine (G140S) amino acid substitutions in integrase that result in clinical INSTI failure perturb optimal magnesium ion coordination in the enzyme active site. The expanded chemical scaffolds of second-generation compounds mediate interactions with the protein backbone that are critical for antagonizing viruses containing the Q148H and G140S mutations. Our results reveal that binding to magnesium ions underpins a fundamental weakness of the INSTI pharmacophore that is exploited by the virus to engender resistance and provide a structural framework for the development of this class of anti-HIV/AIDS therapeutics.
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Affiliation(s)
- Nicola J Cook
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Wen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Dénes Berta
- Department of Chemistry, King's College London, London SE1 1DB, UK
| | - Magd Badaoui
- Department of Chemistry, King's College London, London SE1 1DB, UK
| | | | - Andrea Nans
- Structural Biology Science Technology Platform, Francis Crick Institute, London NW1 1AT, UK
| | - Abhay Kotecha
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, 5651 GG, Netherlands
| | - Edina Rosta
- Department of Chemistry, King's College London, London SE1 1DB, UK
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. .,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London NW1 1AT, UK. .,Department of Infectious Disease, Imperial College London, St Mary's Campus, London W2 1PG, UK
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Papaleo E, Pasi M, Tiberti M, De Gioia L. Molecular dynamics of mesophilic-like mutants of a cold-adapted enzyme: insights into distal effects induced by the mutations. PLoS One 2011; 6:e24214. [PMID: 21915299 PMCID: PMC3168468 DOI: 10.1371/journal.pone.0024214] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 08/02/2011] [Indexed: 11/18/2022] Open
Abstract
Networks and clusters of intramolecular interactions, as well as their "communication" across the three-dimensional architecture have a prominent role in determining protein stability and function. Special attention has been dedicated to their role in thermal adaptation. In the present contribution, seven previously experimentally characterized mutants of a cold-adapted α-amylase, featuring mesophilic-like behavior, have been investigated by multiple molecular dynamics simulations, essential dynamics and analyses of correlated motions and electrostatic interactions. Our data elucidate the molecular mechanisms underlying the ability of single and multiple mutations to globally modulate dynamic properties of the cold-adapted α-amylase, including both local and complex unpredictable distal effects. Our investigation also shows, in agreement with the experimental data, that the conversion of the cold-adapted enzyme in a warm-adapted variant cannot be completely achieved by the introduction of few mutations, also providing the rationale behind these effects. Moreover, pivotal residues, which are likely to mediate the effects induced by the mutations, have been identified from our analyses, as well as a group of suitable candidates for protein engineering. In fact, a subset of residues here identified (as an isoleucine, or networks of mesophilic-like salt bridges in the proximity of the catalytic site) should be considered, in experimental studies, to get a more efficient modification of the features of the cold-adapted enzyme.
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Affiliation(s)
- Elena Papaleo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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Wu XH, Zhang H, Wu YD. Is Asp-His-Ser/Thr-Trp tetrad hydrogen-bond network important to WD40-repeat proteins: a statistical and theoretical study. Proteins 2010; 78:1186-94. [PMID: 19927323 DOI: 10.1002/prot.22638] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
WD40-repeat proteins are abundant and play important roles in forming protein complexes. The domain usually has seven WD40 repeats, which folds into a seven beta-sheet propeller with each beta-sheet in a four-strand structure. An analysis of 20 available WD40-repeat proteins in Protein Data Bank reveals that each protein has at least one Asp-His-Ser/Thr-Trp (D-H-S/T-W) hydrogen-bonded tetrad, and some proteins have up to six or seven such tetrads. The relative positions of the four residues in the tetrads are also found to be conserved. A sequence alignment analysis of 560 WD40-repeat protein sequences in human reveals very similar features, indicating that such tetrad may be a general feature of WD40-repeat proteins. We carried out density functional theory and found that these tetrads can lead to significant stabilization including hydrogen-bonding cooperativity. The hydrogen bond involving Trp is significant. These results lead us to propose that the tetrads may be critical to the stability and the mechanism of folding of these proteins.
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Affiliation(s)
- Xian-Hui Wu
- Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University, Shenzhen, China
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