51
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Tanaka SI, Tsutaki M, Yamamoto S, Mizutani H, Kurahashi R, Hirata A, Takano K. Exploring mutable conserved sites and fatal non-conserved sites by random mutation of esterase from Sulfolobus tokodaii and subtilisin from Thermococcus kodakarensis. Int J Biol Macromol 2020; 170:343-353. [PMID: 33383075 DOI: 10.1016/j.ijbiomac.2020.12.171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
Homologous proteins differ in their amino acid sequences at several positions. Generally, conserved sites are recognized as not suitable for amino acid substitution, and thus in evolutionary protein engineering, non-conserved sites are often selected as mutation sites. However, there have also been reports of possible mutations in conserved sites. In this study, we explored mutable conserved sites and immutable non-conserved sites by testing random mutations of two thermostable proteins, an esterase from Sulfolobus tokodaii (Sto-Est) and a subtilisin from Thermococcus kodakarensis (Tko-Sub). The subtilisin domain of Tko-Sub needs Ca2+ ions and the propeptide domain for stability, folding and maturation. The results from the two proteins showed that about one-third of the mutable sites were detected in conserved sites and some non-conserved sites lost enzymatic activity at high temperatures due to mutation. Of the conserved sites in Sto-Est, the sites on the loop, on the surface, and far from the active site are more resistant to mutation. In Tko-Sub, the sites flanking Ca2+-binding sites and propeptide were undesirable for mutation. The results presented here serve as an index for selecting mutation sites and contribute to the expansion of available sequence range by introducing mutations at conserved sites.
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Affiliation(s)
- Shun-Ichi Tanaka
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Minami Tsutaki
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Seira Yamamoto
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Hayate Mizutani
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Ryo Kurahashi
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Azumi Hirata
- Department of Anatomy and Cell Biology, Osaka Medical College, Daigaku-machi, Takatsuki, Osaka 569-8686, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan.
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52
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Lim W, Siddig E, Eadie K, Nyuykonge B, Ahmed S, Fahal A, Verbon A, Smit S, van de Sande WWJ. The development of a novel diagnostic PCR for Madurella mycetomatis using a comparative genome approach. PLoS Negl Trop Dis 2020; 14:e0008897. [PMID: 33326425 PMCID: PMC7743967 DOI: 10.1371/journal.pntd.0008897] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/17/2020] [Indexed: 12/17/2022] Open
Abstract
Background Eumycetoma is a neglected tropical disease most commonly caused by the fungus Madurella mycetomatis. Identification of eumycetoma causative agents can only be reliably performed by molecular identification, most commonly by species-specific PCR. The current M. mycetomatis specific PCR primers were recently discovered to cross-react with Madurella pseudomycetomatis. Here, we used a comparative genome approach to develop a new M. mycetomatis specific PCR for species identification. Methodology Predicted-protein coding sequences unique to M. mycetomatis were first identified in BLASTCLUST based on E-value, size and presence of orthologues. Primers were then developed for 16 unique sequences and evaluated against 60 M. mycetomatis isolates and other eumycetoma causing agents including the Madurella sibling species. Out of the 16, only one was found to be specific to M. mycetomatis. Conclusion We have discovered a predicted-protein coding sequence unique to M. mycetomatis and have developed a new species-specific PCR to be used as a novel diagnostic marker for M. mycetomatis. Mycetoma is a neglected tropical disease characterised by tumorous swellings and grain formation. This disease can be caused by more than 70 different micro-organisms and is categorised into actinomycetoma (caused by bacteria) and eumycetoma (caused by fungi). The most common causative agent of mycetoma is the fungus Madurella mycetomatis. Diagnosis of eumycetoma is often only done clinically or by histopathological examination and culturing of the grains. Unfortunately, that often leads to misidentifications. Molecular identification is currently the most reliable method to identify the causative agents. However, we have recently discovered that the only M. mycetomatis species-specific PCR primers cross-reacts to Madurella pseudomycetomatis. Since all Madurella species cause eumycetoma and have different susceptibilities to antifungal agents, it is important to be able to accurately identify them to the species level. Here we have used a comparative genome approach to identify and design new M. mycetomatis species-specific PCR primers. These primers can be used to identify M. mycetomatis directly from grains and do not cross-react with any of the other eumycetoma causative agents tested. We, therefore, recommended the use of these primers in reference centres and local laboratories to identify M. mycetomatis to the species level.
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Affiliation(s)
- Wilson Lim
- Erasmus MC, University Medical Center Rotterdam, Department of Microbiology and Infectious Diseases, Rotterdam, The Netherlands
| | - Emmanuel Siddig
- Erasmus MC, University Medical Center Rotterdam, Department of Microbiology and Infectious Diseases, Rotterdam, The Netherlands
- Mycetoma Research Centre, University of Khartoum, Khartoum, Sudan
| | - Kimberly Eadie
- Erasmus MC, University Medical Center Rotterdam, Department of Microbiology and Infectious Diseases, Rotterdam, The Netherlands
| | - Bertrand Nyuykonge
- Erasmus MC, University Medical Center Rotterdam, Department of Microbiology and Infectious Diseases, Rotterdam, The Netherlands
| | - Sarah Ahmed
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Ahmed Fahal
- Mycetoma Research Centre, University of Khartoum, Khartoum, Sudan
| | - Annelies Verbon
- Erasmus MC, University Medical Center Rotterdam, Department of Microbiology and Infectious Diseases, Rotterdam, The Netherlands
| | - Sandra Smit
- Wageningen University & Research, Department of Plant Science, Wageningen, The Netherlands
| | - Wendy WJ van de Sande
- Erasmus MC, University Medical Center Rotterdam, Department of Microbiology and Infectious Diseases, Rotterdam, The Netherlands
- * E-mail:
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53
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Roy C, Mandal SM, Mondal SK, Mukherjee S, Mapder T, Ghosh W, Chakraborty R. Trends of mutation accumulation across global SARS-CoV-2 genomes: Implications for the evolution of the novel coronavirus. Genomics 2020; 112:5331-5342. [PMID: 33161087 PMCID: PMC7644180 DOI: 10.1016/j.ygeno.2020.11.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/22/2022]
Abstract
To understand SARS-CoV-2 microevolution, this study explored the genome-wide frequency, gene-wise distribution, and molecular nature of all point-mutations detected across its 71,703 RNA-genomes deposited in GISAID till 21 August 2020. Globally, nsp1/nsp2 and orf7a/orf3a were the most mutation-ridden non-structural and structural genes respectively. Phylogeny of 4618 spatiotemporally-representative genomes revealed that entities belonging to the early lineages are mostly spread over Asian countries, including India, whereas the recently-derived lineages are more globally distributed. Of the total 20,163 instances of polymorphism detected across global genomes, 12,594 and 7569 involved transitions and transversions, predominated by cytidine-to-uridine and guanosine-to-uridine conversions, respectively. Positive selection of nonsynonymous mutations (dN/dS >1) in most of the structural, but not the non-structural, genes indicated that SARS-CoV-2 has already harmonized its replication/transcription machineries with the host metabolism, while it is still redefining virulence/transmissibility strategies at the molecular level. Mechanistic bases and evolutionary/pathogenicity-related implications are discussed for the predominant mutation-types.
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Affiliation(s)
- Chayan Roy
- College of Veterinary Medicine, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA
| | - Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Suresh K Mondal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Shriparna Mukherjee
- Department of Botany, Prasannadeb Women's College, Jalpaiguri, West Bengal, India
| | - Tarunendu Mapder
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700054, West Bengal, India.
| | - Ranadhir Chakraborty
- Department of Biotechnology, University of North Bengal, Raja Rammohanpur, Darjeeling 734013, West Bengal, India.
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54
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In vitro evolution of antibody affinity via insertional scanning mutagenesis of an entire antibody variable region. Proc Natl Acad Sci U S A 2020; 117:27307-27318. [PMID: 33067389 DOI: 10.1073/pnas.2002954117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We report a systematic combinatorial exploration of affinity enhancement of antibodies by insertions and deletions (InDels). Transposon-based introduction of InDels via the method TRIAD (transposition-based random insertion and deletion mutagenesis) was used to generate large libraries with random in-frame InDels across the entire single-chain variable fragment gene that were further recombined and screened by ribosome display. Knowledge of potential insertion points from TRIAD libraries formed the basis of exploration of length and sequence diversity of novel insertions by insertional-scanning mutagenesis (InScaM). An overall 256-fold affinity improvement of an anti-IL-13 antibody BAK1 as a result of InDel mutagenesis and combination with known point mutations validates this approach, and suggests that the results of this InDel mutagenesis and conventional exploration of point mutations can synergize to generate antibodies with higher affinity.
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55
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S UK, R B, D TK, Doss CGP, Zayed H. Mutational landscape of K-Ras substitutions at 12th position-a systematic molecular dynamics approach. J Biomol Struct Dyn 2020; 40:1571-1585. [PMID: 33034275 DOI: 10.1080/07391102.2020.1830177] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
K-Ras is a small GTPase and acts as a molecular switch by recruiting GEFs and GAPs, and alternates between the inert GDP-bound and the dynamic GTP-bound forms. The amino acid at position 12 of K-Ras is a hot spot for oncogenic mutations (G12A, G12C, G12D, G12R, G12S, and G12V), disturbing the active fold of the protein, leading to cancer development. This study aimed to investigate the potential conformational changes induced by these oncogenic mutations at the 12th position, impairing GAP-mediated GTP hydrolysis. Comprehensive computational tools (iStable, FoldX, SNPeffect, DynaMut, and CUPSAT) were used to evaluate the effect of these six mutations on the stability of wild type K-Ras protein. The docking of GTP with K-Ras was carried out using AutoDock4.2, followed by molecular dynamics simulations. Furthermore, on comparison of binding energies between the wild type K-Ras and the six mutants, we have demonstrated that the G12A and G12V mutants exhibited the strongest binding efficiency compared to the other four mutants. Trajectory analyses of these mutations revealed that G12A encountered the least deviation, fluctuation, intermolecular H-bonds, and compactness compared to the wildtype, which was supported by the lower Gibbs free energy value. Our study investigates the molecular dynamics simulations of the mutant K-Ras forms at the 12th position, which expects to provide insights about the molecular mechanisms involved in cancer development, and may serve as a platform for targeted therapies against cancer. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Udhaya Kumar S
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Bithia R
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Thirumal Kumar D
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar
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56
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Qiu H, Qin A, Cheng T, Chim SM, Smithers L, Chen K, Song D, Liu Q, Zhao J, Wang C, Teguh D, Zhang G, Tickner J, Vrielink A, Pavlos NJ, Xu J. A missense mutation sheds light on a novel structure-function relationship of RANKL. J Cell Physiol 2020; 236:2800-2816. [PMID: 32964459 DOI: 10.1002/jcp.30045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 12/18/2022]
Abstract
The tumor necrosis factor (TNF)-like core domain of receptor activator of nuclear factor-κB ligand (RANKL) is a functional domain critical for osteoclast differentiation. One of the missense mutations identified in patients with osteoclast-poor autosomal recessive osteopetrosis (ARO) is located in residue methionine 199 that is replaced with lysine (M199K) amid the TNF-like core domain. However, the structure-function relationship of this mutation is not clear. Sequence-based alignment revealed that the fragment containing human M199 is highly conserved and equivalent to M200 in rat. Using site-directed mutagenesis, we generated three recombinant RANKL mutants M200K/A/E (M200s) by replacing the methionine 200 with lysine (M200K), alanine (M200A), and glutamic acid (M200E), representative of distinct physical properties. TRAcP staining and bone pit assay showed that M200s failed to support osteoclast formation and bone resorption, accompanied by impaired osteoclast-related signal transduction. However, no antagonistic effect was found in M200s against wild-type rat RANKL. Analysis of the crystal structure of RANKL predicted that this methionine residue is located within the hydrophobic core of the protein, thus, likely to be crucial for protein folding and stability. Consistently, differential scanning fluorimetry analysis suggested that M200s were less stable. Western blot analysis analyses further revealed impaired RANKL trimerization by M200s. Furthermore, receptor-ligand binding assay displayed interrupted interaction of M200s to its intrinsic receptors. Collectively, our studies revealed the molecular basis of human M199-induced ARO and elucidated the indispensable role of rodent residue M200 (equivalent to human M199) for the RANKL function.
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Affiliation(s)
- Heng Qiu
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - An Qin
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia.,Shanghai Key Laboratory of Orthopaedic Implant, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Taksum Cheng
- Bone Biology and Disease Laboratory, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Shek M Chim
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Luke Smithers
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kai Chen
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Dezhi Song
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia.,Department of Research Centre for Regenerative Medicine, Guangxi Medical University, Nanning, China
| | - Qian Liu
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia.,Department of Research Centre for Regenerative Medicine, Guangxi Medical University, Nanning, China
| | - Jinmin Zhao
- Department of Research Centre for Regenerative Medicine, Guangxi Medical University, Nanning, China
| | - Chao Wang
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Dian Teguh
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Ge Zhang
- School of Chinese Medicine, Institute for Advancing Translational Medicine in Bone and Joint Diseases, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Jennifer Tickner
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Alice Vrielink
- School of Molecular Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Nathan J Pavlos
- Bone Biology and Disease Laboratory, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Jiake Xu
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
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57
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Prathiviraj R, Chellapandi P. Deciphering Molecular Virulence Mechanism of Mycobacterium tuberculosis Dop isopeptidase Based on Its Sequence-Structure-Function Linkage. Protein J 2020; 39:33-45. [PMID: 31760575 DOI: 10.1007/s10930-019-09876-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The pupylation pathway marks proteins for prokaryotic ubiquitin-like protein (Pup)-proteasomal degradation and survival strategy of mycobacteria inside of the host macrophages. Deamidase of Pup (Dop) plays a central role in the pupylation pathway. It is still a matter of investigation to know the function of Dop in virulence of mycobacterial lineage. Hence, the present study was intended to describe the sequence-structure-function-virulence link of Dop for understanding the molecular virulence mechanism of Mycobacterium tuberculosis H37Rv (Mtb). Phylogenetic analysis of this study indicated that Dop has extensively diverged across the proteasome-harboring bacteria. The functional part of Dop was converged across the pathogenic mycobacterial lineage. The genome-wide analysis pointed out that the pupylation gene locus was identical to each other, but its genome neighborhood differed from species to species. Molecular modeling and dynamic studies proved that the predicted structure of Mtb Dop was energetically stable and low conformational freedom. Moreover, evolutionary constraints in Mtb Dop were intensively analyzed for inferring its sequence-structure-function relationships for the full virulence of Mtb. It indicated that evolutionary optimization was extensively required to stabilize its local structural environment at the side chains of mutable residues. The sequence-structure-function-virulence link of Dop might have retained in Mtb by reordering hydrophobic and hydrogen bonding patterns in the local structural environment. Thus, the results of our study provide a quest to understand the molecular virulence and pathogenesis mechanisms of Mtb during the infection process.
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Affiliation(s)
- R Prathiviraj
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024, India.
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58
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Carpentier M, Chomilier J. Analyses of displacements resulting from a point mutation in proteins. J Struct Biol 2020; 211:107543. [PMID: 32522553 DOI: 10.1016/j.jsb.2020.107543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/28/2020] [Accepted: 05/31/2020] [Indexed: 11/19/2022]
Abstract
The effects of a single residue substitution on the protein backbone are frequently quite small and there are many other potential sources of structural variation for protein. We present here a methodology considering different sources of distortions in order to isolate the very effect of the mutation. To validate our methodology, we consider a well-studied family with many single mutants: the human lysozyme. Most of the perturbations are expected to be at the very localisation of the mutation, but in many cases the effects are propagated at long range. We show that the distances between the mutated residue and the 5% most disturbed residues exponentially decreases. One third of the affected residues are in direct contact with the mutated position; the remaining two thirds are potential allosteric effects. We confirm the reliability of the residues identified as significantly perturbed by comparing our results to experimental studies. We confirm with the present method all the previously identified perturbations. This study shows that mutations have long-range impact on protein backbone that can be detected, although the displacement of the affected atoms is small.
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Affiliation(s)
- Mathilde Carpentier
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, 57 rue Cuvier, CP 50, 75005 Paris, France.
| | - Jacques Chomilier
- Sorbonne Université, BiBiP IMPMC UMR 7590, CNRS, MNHN, Paris, France.
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59
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Emond S, Petek M, Kay EJ, Heames B, Devenish SRA, Tokuriki N, Hollfelder F. Accessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis. Nat Commun 2020; 11:3469. [PMID: 32651386 PMCID: PMC7351745 DOI: 10.1038/s41467-020-17061-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 06/01/2020] [Indexed: 11/22/2022] Open
Abstract
Insertions and deletions (InDels) are frequently observed in natural protein evolution, yet their potential remains untapped in laboratory evolution. Here we introduce a transposon-based mutagenesis approach (TRIAD) to generate libraries of random variants with short in-frame InDels, and screen TRIAD libraries to evolve a promiscuous arylesterase activity in a phosphotriesterase. The evolution exhibits features that differ from previous point mutagenesis campaigns: while the average activity of TRIAD variants is more compromised, a larger proportion has successfully adapted for the activity. Different functional profiles emerge: (i) both strong and weak trade-off between activities are observed; (ii) trade-off is more severe (20- to 35-fold increased kcat/KM in arylesterase with 60-400-fold decreases in phosphotriesterase activity) and (iii) improvements are present in kcat rather than just in KM, suggesting adaptive solutions. These distinct features make TRIAD an alternative to widely used point mutagenesis, accessing functional innovations and traversing unexplored fitness landscape regions.
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Affiliation(s)
- Stephane Emond
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
- Evonetix Ltd, Coldhams Business Park, Norman Way, Cambridge, CB1 3LH, UK.
| | - Maya Petek
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Emily J Kay
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Brennen Heames
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149, Münster, Germany
| | - Sean R A Devenish
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Fluidic Analytics, The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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60
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Marabotti A, Scafuri B, Facchiano A. Predicting the stability of mutant proteins by computational approaches: an overview. Brief Bioinform 2020; 22:5850907. [PMID: 32496523 DOI: 10.1093/bib/bbaa074] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 01/06/2023] Open
Abstract
A very large number of computational methods to predict the change in thermodynamic stability of proteins due to mutations have been developed during the last 30 years, and many different web servers are currently available. Nevertheless, most of them suffer from severe drawbacks that decrease their general reliability and, consequently, their applicability to different goals such as protein engineering or the predictions of the effects of mutations in genetic diseases. In this review, we have summarized all the main approaches used to develop these tools, with a survey of the web servers currently available. Moreover, we have also reviewed the different assessments made during the years, in order to allow the reader to check directly the different performances of these tools, to select the one that best fits his/her needs, and to help naïve users in finding the best option for their needs.
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61
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A Single Gene Causes Thelytokous Parthenogenesis, the Defining Feature of the Cape Honeybee Apis mellifera capensis. Curr Biol 2020; 30:2248-2259.e6. [DOI: 10.1016/j.cub.2020.04.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/05/2020] [Accepted: 04/15/2020] [Indexed: 02/01/2023]
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62
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Miller M, Vitale D, Kahn PC, Rost B, Bromberg Y. funtrp: identifying protein positions for variation driven functional tuning. Nucleic Acids Res 2020; 47:e142. [PMID: 31584091 PMCID: PMC6868392 DOI: 10.1093/nar/gkz818] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/05/2019] [Accepted: 09/12/2019] [Indexed: 12/12/2022] Open
Abstract
Evaluating the impact of non-synonymous genetic variants is essential for uncovering disease associations and mechanisms of evolution. An in-depth understanding of sequence changes is also fundamental for synthetic protein design and stability assessments. However, the variant effect predictor performance gain observed in recent years has not kept up with the increased complexity of new methods. One likely reason for this might be that most approaches use similar sets of gene and protein features for modeling variant effects, often emphasizing sequence conservation. While high levels of conservation highlight residues essential for protein activity, much of the variation observable in vivo is arguably weaker in its impact, thus requiring evaluation at a higher level of resolution. Here, we describe functionNeutral/Toggle/Rheostatpredictor (funtrp), a novel computational method that categorizes protein positions based on the position-specific expected range of mutational impacts: Neutral (weak/no effects), Rheostat (function-tuning positions), or Toggle (on/off switches). We show that position types do not correlate strongly with familiar protein features such as conservation or protein disorder. We also find that position type distribution varies across different protein functions. Finally, we demonstrate that position types can improve performance of existing variant effect predictors and suggest a way forward for the development of new ones.
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Affiliation(s)
- Maximilian Miller
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08901, USA
| | - Daniel Vitale
- Columbian College of Arts and Sciences Data Science Program Corcoran Hall, 725 21st Street NW, Washington, DC 20052, USA
| | - Peter C Kahn
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08901, USA
| | - Burkhard Rost
- Department for Bioinformatics and Computational Biology, Technische Universität München, Boltzmannstr. 3, 85748 Garching/Munich, Germany.,Institute for Advanced Study at Technische Universität München (TUM-IAS), Lichtenbergstraße 2a 85748 Garching/Munich, Germany
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08901, USA.,Institute for Advanced Study at Technische Universität München (TUM-IAS), Lichtenbergstraße 2a 85748 Garching/Munich, Germany.,Department of Genetics, Rutgers University, Human Genetics Institute, Life Sciences Building, 145 Bevier Road, Piscataway, NJ 08854, USA
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63
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Shaik NA, Nasser KK, Alruwaili MM, Alallasi SR, Elango R, Banaganapalli B. Molecular modelling and dynamic simulations of sequestosome 1 (SQSTM1) missense mutations linked to Paget disease of bone. J Biomol Struct Dyn 2020; 39:2873-2884. [PMID: 32329415 DOI: 10.1080/07391102.2020.1758212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The Paget disease (PDB; OMIM is 167250) is a chronic bone disease caused by pathogenic mutations in Sequestome1/p62 (SQSTM1) gene. This study has aimed to interpret the relationship of PDB linked SQSTM1 mutations with protein structure and its molecular dynamic features. The disease causative missense mutations were initially collected, and then analyzed for their, exonic and domain distribution, impact on secondary and tertiary structures, and their ability on protein-ligand interactions, using a combination of systems biology approaches. Our results show that most PDB linked SQSTM1 missense mutations affect amino acid residues clustered within or near the UBA domain (aa 389-434), which participates in the ubiquitination of substrates. We also report that the majority mutations occurred in α-helices over β-strands but their effects on the secondary structure were mostly neutral. Global tertiary structure deviations were minimal; however, at amino acid residue level minor structural changes were evident. The molecular dynamics simulation analysis showed that both PB1 and UBA domains were under constant structural fluctuations resulting in closed form conformation of SQSMT1 protein structure, when it is bound to PRKCI ligand. We also found salt bridge conformation changes in the UBA domain of SQSTM1 mutants when they bound to the PRKCI interactor protein. This finding suggests the possibility that mutations in SQSTM1 could impair its ability to ubiquitinate the substrates, eventually affecting autophagy and apoptosis, especially in mature osteoclasts. This study presents the additional insight into structure and function relationship between SQSTM1 mutations and PDB pathogenesis. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Noor Ahmad Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalidah K Nasser
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muteb Muidh Alruwaili
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia
| | - Sami Raja Alallasi
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Saudi Arabia.,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
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64
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Sinha S, Wang SM. Classification of VUS and unclassified variants in BRCA1 BRCT repeats by molecular dynamics simulation. Comput Struct Biotechnol J 2020; 18:723-736. [PMID: 32257056 PMCID: PMC7125325 DOI: 10.1016/j.csbj.2020.03.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 10/29/2022] Open
Abstract
Pathogenic mutation in BRCA1 gene is one of the most penetrant genetic predispositions towards cancer. Identification of the mutation provides important aspect in prevention and treatment of the mutation-caused cancer. Of the large quantity of genetic variants identified in human BRCA1, substantial portion is classified as Variant of Uncertain Significance (VUS) or unclassified variants due to the lack of functional evidence. In this study, we focused on the VUS and unclassified variants in BRCT repeat located at BRCA1 C-terminal. Utilizing the well-determined structure of BRCT repeats, we measured the influence of the variants on the structural conformations of BRCT repeats by using molecular dynamics simulation (MDS) consisting of RMSD (Root-mean-square-deviation), RMSF (Root-mean-square-fluctuations), Rg (Radius of gyration), SASA (Solvent accessible surface area), NH bond (hydrogen bond) and Covariance analysis. Using this approach, we analyzed 131 variants consisting of 89 VUS (Variant of Uncertain Significance) and 42 unclassified variants (unclassifiable by current methods) within BRCT repeats and were able to differentiate them into 78 Deleterious and 53 Tolerated variants. Comparing the results made by the saturation genome editing assay, multiple experimental assays, and BRCA1 reference databases shows that our approach provides high specificity, sensitivity and robust. Our study opens an avenue to classify VUS and unclassified variants in many cancer predisposition genes with known protein structure.
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Affiliation(s)
- Siddharth Sinha
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - San Ming Wang
- Cancer Centre and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
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65
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Udhaya Kumar S, Thirumal Kumar D, Mandal PD, Sankar S, Haldar R, Kamaraj B, Walter CEJ, Siva R, George Priya Doss C, Zayed H. Comprehensive in silico screening and molecular dynamics studies of missense mutations in Sjogren-Larsson syndrome associated with the ALDH3A2 gene. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 120:349-377. [PMID: 32085885 DOI: 10.1016/bs.apcsb.2019.11.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sjögren-Larsson syndrome (SLS) is an autoimmune disorder inherited in an autosomal recessive pattern. To date, 80 missense mutations have been identified in association with the Aldehyde Dehydrogenase 3 Family Member A2 (ALDH3A2) gene causing SLS. Disruption of the function of ALDH3A2 leads to excessive accumulation of fat in the cells, which interferes with the normal function of protective membranes or materials that are necessary for the body to function normally. We retrieved 54 missense mutations in the ALDH3A2 from the OMIM, UniProt, dbSNP, and HGMD databases that are known to cause SLS. These mutations were examined with various in silico stability tools, which predicted that the mutations p.S308N and p.R423H that are located at the protein-protein interaction domains are the most destabilizing. Furthermore, to determine the atomistic-level differences within the protein-protein interactions owing to mutations, we performed macromolecular simulation (MMS) using GROMACS to validate the motion patterns and dynamic behavior of the biological system. We found that both mutations (p.S380N and p.R423H) had significant effects on the protein-protein interaction and disrupted the dimeric interactions. The computational pipeline provided in this study helps to elucidate the potential structural and functional differences between the ALDH3A2 native and mutant homodimeric proteins, and will pave the way for drug discovery against specific targets in the SLS patients.
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Affiliation(s)
- S Udhaya Kumar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - D Thirumal Kumar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Pinky D Mandal
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Srivarshini Sankar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Rishin Haldar
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Balu Kamaraj
- Department of Neuroscience Technology, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia
| | - Charles Emmanuel Jebaraj Walter
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (Deemed to be University), Chennai, India
| | - R Siva
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C George Priya Doss
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar
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66
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Li D, Ji B. Protein conformational transitions coupling with ligand interactions: Simulations from molecules to medicine. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2019. [DOI: 10.1016/j.medntd.2019.100026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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67
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Rodríguez-Ruiz HA, Garibay-Cerdenares OL, Illades-Aguiar B, Montaño S, Jiang X, Leyva-Vázquez MA. In silico prediction of structural changes in human papillomavirus type 16 (HPV16) E6 oncoprotein and its variants. BMC Mol Cell Biol 2019; 20:35. [PMID: 31426742 PMCID: PMC6700771 DOI: 10.1186/s12860-019-0217-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/08/2019] [Indexed: 12/11/2022] Open
Abstract
Background HPV16 infection is one of the main risk factors involved in the development of cervical cancer, mainly due to the high oncogenic potential of the viral proteins E6 and E7, which are involved in the different processes of malignant transformation. There is a broad spectrum of intratypical variation of E6, which is reflected in its high diversity, biological behavior, global distribution and risk of causing cervical cancer. Experimental studies have shown that the intratypical variants of the protein E6 from the European variants (E-G350, E-A176/G350, E-C188/G350) and Asian-American variants (AAa and AAc), are capable of inducing the differential expression of genes involved in the development of cervical cancer. Results An in silico analysis was performed to characterize the molecular effects of these variations using the structure of the HPV16 E6 oncoprotein (PDB: 4XR8; chain H) as a template. In particular, we evaluated the 3D structures of the intratypical variants by structural alignment, ERRAT, Ramachandran plots and prediction of protein disorder, which was further validated by molecular dynamics simulations. Our results, in general, showed no significant changes in the protein 3D structure. However, we observed subtle changes in protein physicochemical features and structural disorder in the N- and C-termini. Conclusions Our results showed that mutations in the viral oncogene E6 of six high-risk HPV16 variants are effectively neutral and do not cause significant structural changes except slight variations of structural disorder. As structural disorder is involved in rewiring protein-protein interactions, these results suggest a differential pattern of interaction of E6 with the target protein P53 and possibly different patterns of tumor aggressiveness associated with certain types of variants of the E6 oncoprotein. Electronic supplementary material The online version of this article (10.1186/s12860-019-0217-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hugo Alberto Rodríguez-Ruiz
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Mexico
| | - Olga Lilia Garibay-Cerdenares
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Mexico.,CONACyT-Autonomous University of Guerrero, Chilpancingo, Mexico
| | - Berenice Illades-Aguiar
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Mexico
| | - Sarita Montaño
- Faculty of Chemical and Biological Sciences, Autonomous University of Sinaloa, Culiacan, Mexico
| | - Xiaowei Jiang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China. .,Guangzhou-Birmingham Joint Research Center for Birth Cohorts and Disease Cohorts, Guangzhou Medical University, Guangzhou, China. .,Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Marco Antonio Leyva-Vázquez
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Mexico.
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68
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Prisilla A, Chellapandi P. Cloning and expression of immunogenic Clostridium botulinum C2I mutant proteins designed from their evolutionary imprints. Comp Immunol Microbiol Infect Dis 2019; 65:207-212. [DOI: 10.1016/j.cimid.2019.01.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 12/15/2018] [Accepted: 01/14/2019] [Indexed: 01/11/2023]
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69
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Syed Haneef SA, Ranganathan S. Structural bioinformatics analysis of variants on GPCR function. Curr Opin Struct Biol 2019; 55:161-177. [PMID: 31174013 DOI: 10.1016/j.sbi.2019.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 10/26/2022]
Abstract
G protein-coupled receptors (GPCRs) are key membrane-embedded receptor proteins, with critical roles in cellular signal transduction. In the era of precision medicine, understanding the role of natural variants on GPCR function is critical, especially from a pharmacogenomics viewpoint. Studies involved in mapping variants to GPCR structures are briefly reviewed here. The endocannabinoid system involving the central nervous system (CNS), the human cannabinoid receptor 1 (CB1), is an important drug target and its variability has implications for disease susceptibility and altered drug and pain response. We have carried out a computational study to map deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) to CB1. CB1 mutations were computationally evaluated from neutral to deleterious, and the top twelve deleterious mutations, with structural information, were found to be either close to the ligand binding region or the G-protein binding site. We have mapped these to the active and inactive CB1 X-ray crystallographic structures to correlate variants with available phenotypic information. We have also carried out molecular dynamics simulations to functionally characterize four selected mutants.
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Affiliation(s)
- Syed Askar Syed Haneef
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia.
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70
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Bradley D, Beltrao P. Evolution of protein kinase substrate recognition at the active site. PLoS Biol 2019; 17:e3000341. [PMID: 31233486 PMCID: PMC6611643 DOI: 10.1371/journal.pbio.3000341] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/05/2019] [Accepted: 06/12/2019] [Indexed: 02/05/2023] Open
Abstract
Protein kinases catalyse the phosphorylation of target proteins, controlling most cellular processes. The specificity of serine/threonine kinases is partly determined by interactions with a few residues near the phospho-acceptor residue, forming the so-called kinase-substrate motif. Kinases have been extensively duplicated throughout evolution, but little is known about when in time new target motifs have arisen. Here, we show that sequence variation occurring early in the evolution of kinases is dominated by changes in specificity-determining residues. We then analysed kinase specificity models, based on known target sites, observing that specificity has remained mostly unchanged for recent kinase duplications. Finally, analysis of phosphorylation data from a taxonomically broad set of 48 eukaryotic species indicates that most phosphorylation motifs are broadly distributed in eukaryotes but are not present in prokaryotes. Overall, our results suggest that the set of eukaryotes kinase motifs present today was acquired around the time of the eukaryotic last common ancestor and that early expansions of the protein kinase fold rapidly explored the space of possible target motifs.
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Affiliation(s)
- David Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
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71
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Naqvi AAT, Alajmi MF, Rehman T, Hussain A, Hassan I. Effects of Pro1266Leu mutation on structure and function of glycoprotein Ib binding domain of von Willebrand factor. J Cell Biochem 2019; 120:17847-17857. [PMID: 31135071 DOI: 10.1002/jcb.29052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023]
Abstract
Glycoprotein Ibα (GpIbα) binding ability of A1 domain of von Willebrand factor (vWF) facilitates platelet adhesion that plays a crucial role in maintaining hemostasis and thrombosis at the site of vascular damage. There are both "loss as well as gain of function" mutations observed in this domain. Naturally occurring "gain of function" mutations leave self-activating impacts on the A1 domain which turns the normal binding to characteristic constitutive binding with GPIbα. These "gain of function" mutations are associated with the von Willebrand disease type 2B. In recent years, studies focused on understanding the mechanism and conformational patterns attached to these phenomena have been conducted, but the conformational pathways leading to such binding patterns are poorly understood as of now. To obtain a microscopic picture of such events for the better understanding of pathways, we used molecular dynamics (MD) simulations along with principal component analysis and normal mode analysis to study the effects of Pro1266Leu (Pro503Leu in structural context) mutation on the structure and function of A1 domain of vWF. MD simulations have provided atomic-level details of intermolecular motions as a function of time to understand the dynamic behavior of A1 domain of vWF. Comparative analysis of the trajectories obtained from MD simulations of both the wild type and Pro503Leu mutant suggesting appreciable conformational changes in the structure of mutant which might provide a basis for assuming the "gain of function" effects of these mutations on the A1 domain of vWF, resulting in the constitutive binding with GpIbα.
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Affiliation(s)
- Ahmad Abu Turab Naqvi
- Center for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Tabish Rehman
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, KSA
| | - Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Science, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
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72
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Stiers KM, Graham AC, Zhu JS, Jakeman DL, Nix JC, Beamer LJ. Structural and dynamical description of the enzymatic reaction of a phosphohexomutase. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:024703. [PMID: 31041362 PMCID: PMC6443537 DOI: 10.1063/1.5092803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Enzymes are known to adopt various conformations at different points along their catalytic cycles. Here, we present a comprehensive analysis of 15 isomorphous, high resolution crystal structures of the enzyme phosphoglucomutase from the bacterium Xanthomonas citri. The protein was captured in distinct states critical to function, including enzyme-substrate, enzyme-product, and enzyme-intermediate complexes. Key residues in ligand recognition and regions undergoing conformational change are identified and correlated with the various steps of the catalytic reaction. In addition, we use principal component analysis to examine various subsets of these structures with two goals: (1) identifying sites of conformational heterogeneity through a comparison of room temperature and cryogenic structures of the apo-enzyme and (2) a priori clustering of the enzyme-ligand complexes into functionally related groups, showing sensitivity of this method to structural features difficult to detect by traditional methods. This study captures, in a single system, the structural basis of diverse substrate recognition, the subtle impact of covalent modification, and the role of ligand-induced conformational change in this representative enzyme of the α-D-phosphohexomutase superfamily.
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Affiliation(s)
- Kyle M. Stiers
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA
| | - Abigail C. Graham
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA
| | - Jian-She Zhu
- College of Pharmacy, Dalhousie University, 5968 College Street, Halifax, Nova Scotia B3H 3J5, Canada
| | | | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Lesa J. Beamer
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, USA
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73
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Oyiga BC, Ogbonnaya FC, Sharma RC, Baum M, Léon J, Ballvora A. Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:323-346. [PMID: 30392081 PMCID: PMC6349800 DOI: 10.1007/s00122-018-3220-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/24/2018] [Indexed: 05/02/2023]
Abstract
SNP alleles on chromosomes 4BL and 6AL are associated with sensitivity to salt tolerance in wheat and upon validation can be exploited in the development of salt-tolerant wheat varieties. The dissection of the genetic and molecular components of salt stress response offers strong opportunities toward understanding and improving salt tolerance in crops. In this study, GWAS was employed to identify a total of 106 SNP loci (R2 = 0.12-63.44%) linked to salt stress response in wheat using leaf chlorophyll fluorescence, grain quality and shoot ionic (Na+ and K+ ions) attributes. Among them, 14 SNP loci individually conferred pleiotropic effects on multiple independent salinity tolerance traits including loci at 99.04 cM (R2 ≥ 14.7%) and 68.45 cM (R2 ≥ 4.10%) on chromosomes 6AL and 4BL, respectively, that influenced shoot Na+-uptake, shoot K+/Na+ ratio, and specific energy fluxes for absorption (ABS/RC) and dissipation (DIo/RC). Analysis of the open reading frame (ORF) containing the SNP markers revealed that they are orthologous to genes involved in photosynthesis and plant stress (salt) response. Further transcript abundance and qRT-PCR analyses indicated that the genes are mostly up-regulated in salt-tolerant and down-regulated in salt-sensitive wheat genotypes including NRAMP-2 and OPAQUE1 genes on 4BL and 6AL, respectively. Both genes showed highest differential expression between contrasting genotypes when expressions of all the genes within their genetic intervals were analyzed. Possible cis-acting regulatory elements and coding sequence variation that may be involved in salt stress response were also identified in both genes. This study identified genetic and molecular components of salt stress response that are associated with Na+-uptake, shoot Na+/K+ ratio, ABS/RC, DIo/RC, and grain quality traits and upon functional validation would facilitate the development of gene-specific markers that could be deployed to improve salinity tolerance in wheat.
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Affiliation(s)
- Benedict C Oyiga
- INRES-Pflanzenzuchtung, Rheinische Friedrich-Wilhelms-Universitat, Bonn, Germany
- Center for Development Research (ZEF), Rheinische Friedrich-Wilhelms-Universitat, Bonn, Germany
| | | | - Ram C Sharma
- International Center for Agricultural Research in the Dry Areas (ICARDA), Tashkent, Uzbekistan
| | - Michael Baum
- International Centre for Agricultural Research in the Dry Areas (ICARDA), Al Irfane, 10112, Rabat, Morocco
| | - Jens Léon
- INRES-Pflanzenzuchtung, Rheinische Friedrich-Wilhelms-Universitat, Bonn, Germany
| | - Agim Ballvora
- INRES-Pflanzenzuchtung, Rheinische Friedrich-Wilhelms-Universitat, Bonn, Germany.
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74
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Peng Y, Alexov E, Basu S. Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases. Int J Mol Sci 2019; 20:ijms20030548. [PMID: 30696058 PMCID: PMC6386852 DOI: 10.3390/ijms20030548] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 01/25/2019] [Accepted: 01/26/2019] [Indexed: 12/25/2022] Open
Abstract
Structural information of biological macromolecules is crucial and necessary to deliver predictions about the effects of mutations-whether polymorphic or deleterious (i.e., disease causing), wherein, thermodynamic parameters, namely, folding and binding free energies potentially serve as effective biomarkers. It may be emphasized that the effect of a mutation depends on various factors, including the type of protein (globular, membrane or intrinsically disordered protein) and the structural context in which it occurs. Such information may positively aid drug-design. Furthermore, due to the intrinsic plasticity of proteins, even mutations involving radical change of the structural and physico⁻chemical properties of the amino acids (native vs. mutant) can still have minimal effects on protein thermodynamics. However, if a mutation causes significant perturbation by either folding or binding free energies, it is quite likely to be deleterious. Mitigating such effects is a promising alternative to the traditional approaches of designing inhibitors. This can be done by structure-based in silico screening of small molecules for which binding to the dysfunctional protein restores its wild type thermodynamics. In this review we emphasize the effects of mutations on two important biophysical properties, stability and binding affinity, and how structures can be used for structure-based drug design to mitigate the effects of disease-causing variants on the above biophysical properties.
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Affiliation(s)
- Yunhui Peng
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
| | - Sankar Basu
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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75
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Dasmeh P, Serohijos AWR. Estimating the contribution of folding stability to nonspecific epistasis in protein evolution. Proteins 2018; 86:1242-1250. [DOI: 10.1002/prot.25588] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/28/2018] [Accepted: 07/18/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Pouria Dasmeh
- Department of BiochemistryUniversity of Montreal Montreal Quebec Canada
- Cedergren Center for Bioinformatics and GenomicsUniversity of Montreal Montreal, Quebec Canada
- Department of Biochemistry and Institute for Data Valorization (IVADO)University of Montreal Montreal, Quebec Canada
| | - Adrian W. R. Serohijos
- Department of BiochemistryUniversity of Montreal Montreal Quebec Canada
- Cedergren Center for Bioinformatics and GenomicsUniversity of Montreal Montreal, Quebec Canada
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76
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Brown AP, Arias-Rodriguez L, Yee MC, Tobler M, Kelley JL. Concordant Changes in Gene Expression and Nucleotides Underlie Independent Adaptation to Hydrogen-Sulfide-Rich Environments. Genome Biol Evol 2018; 10:2867-2881. [PMID: 30215710 PMCID: PMC6225894 DOI: 10.1093/gbe/evy198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2018] [Indexed: 12/23/2022] Open
Abstract
The colonization of novel environments often involves changes in gene expression, protein coding sequence, or both. Studies of how populations adapt to novel conditions, however, often focus on only one of these two processes, potentially missing out on the relative importance of different parts of the evolutionary process. In this study, our objectives were 1) to better understand the qualitative concordance between conclusions drawn from analyses of differential expression and changes in genic sequence and 2) to quantitatively test whether differentially expressed genes were enriched for sites putatively under positive selection within gene regions. To achieve this, we compared populations of fish (Poecilia mexicana) that have independently adapted to hydrogen-sulfide-rich environments in southern Mexico to adjacent populations residing in nonsulfidic waters. Specifically, we used RNA-sequencing data to compare both gene expression and DNA sequence differences between populations. Analyzing these two different data types led to similar conclusions about which biochemical pathways (sulfide detoxification and cellular respiration) were involved in adaptation to sulfidic environments. Additionally, we found a greater overlap between genes putatively under selection and differentially expressed genes than expected by chance. We conclude that considering both differential expression and changes in DNA sequence led to a more comprehensive understanding of how these populations adapted to extreme environmental conditions. Our results imply that changes in both gene expression and DNA sequence-sometimes at the same loci-may be involved in adaptation.
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Affiliation(s)
- Anthony P Brown
- School of Biological Sciences, Washington State University, 100 Dairy Road, Pullman, WA 99164
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), C.P. 86150, Villahermosa, Tabasco, México
| | - Muh-Ching Yee
- Stanford Functional Genomics Facility, CCSR 0120, Stanford, CA 94305
| | - Michael Tobler
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, 100 Dairy Road, Pullman, WA 99164
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77
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Zhang Z, Wang J, Gong Y, Li Y. Contributions of substitutions and indels to the structural variations in ancient protein superfamilies. BMC Genomics 2018; 19:771. [PMID: 30355304 PMCID: PMC6201574 DOI: 10.1186/s12864-018-5178-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/16/2018] [Indexed: 11/10/2022] Open
Abstract
Background Quantitative evaluation of protein structural evolution is important for our understanding of protein biological functions and their evolutionary adaptation, and is useful in guiding protein engineering. However, compared to the models for sequence evolution, the quantitative models for protein structural evolution received less attention. Ancient protein superfamilies are often considered versatile, allowing genetic and functional diversifications during long-term evolution. In this study, we investigated the quantitative impacts of sequence variations on the structural evolution of homologues in 68 ancient protein superfamilies that exist widely in sequenced eukaryotic, bacterial and archaeal genomes. Results We found that the accumulated structural variations within ancient superfamilies could be explained largely by a bilinear model that simultaneously considers amino acid substitution and insertion/deletion (indel). Both substitutions and indels are essential for explaining the structural variations within ancient superfamilies. For those ancient superfamilies with high bilinear multiple correlation coefficients, the influence of each unit of substitution or indel on structural variations is almost constant within each superfamily, but varies greatly among different superfamilies. The influence of each unit indel on structural variations is always larger than that of each unit substitution within each superfamily, but the accumulated contributions of indels to structural variations are lower than those of substitutions in most superfamilies. The total contributions of sequence indels and substitutions (46% and 54%, respectively) to the structural variations that result from sequence variations are slightly different in ancient superfamilies. Conclusions Structural variations within ancient protein superfamilies accumulated under the significantly bilinear influence of amino acid substitutions and indels in sequences. Both substitutions and indels are essential for explaining the structural variations within ancient superfamilies. For those structural variations resulting from sequence variations, the total contribution of indels is slightly lower than that of amino acid substitutions. The regular clock exists not only in protein sequences, but also probably in protein structures. Electronic supplementary material The online version of this article (10.1186/s12864-018-5178-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zheng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jinlan Wang
- Physical Examination Office of Shandong Province, Health and Family Planning Commission of Shandong Province, Jinan, 250014, China
| | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
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78
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Jimenez-Rosales A, Flores-Merino MV. Tailoring Proteins to Re-Evolve Nature: A Short Review. Mol Biotechnol 2018; 60:946-974. [DOI: 10.1007/s12033-018-0122-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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79
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Topology of active, membrane-embedded Bax in the context of a toroidal pore. Cell Death Differ 2018; 25:1717-1731. [PMID: 30185826 DOI: 10.1038/s41418-018-0184-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/20/2018] [Accepted: 05/21/2018] [Indexed: 01/18/2023] Open
Abstract
Bax is a Bcl-2 protein critical for apoptosis induction. In healthy cells, Bax is mostly a monomeric, cytosolic protein, while upon apoptosis initiation it inserts into the outer mitochondrial membrane, oligomerizes, and forms pores that release proapoptotic factors like Cytochrome c into the cytosol. The structures of active Bax and its homolog Bak are only partially understood and the topology of the proteins with respect to the membrane bilayer is controversially described in the literature. Here, we systematically review and examine the protein-membrane, protein-water, and protein-protein contacts of the nine helices of active Bax and Bak, and add a new set of topology data obtained by fluorescence and EPR methods. We conclude based on the consistent part of the datasets that the core/dimerization domain of Bax (Bak) is water exposed with only helices 4 and 5 in membrane contact, whereas the piercing/latch domain is in peripheral membrane contact, with helix 9 being transmembrane. Among the available structural models, those considering the dimerization/core domain at the rim of a toroidal pore are the most plausible to describe the active state of the proteins, although the structural flexibility of the piercing/latch domain does not allow unambiguous discrimination between the existing models.
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80
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Trade-offs with stability modulate innate and mutationally acquired drug resistance in bacterial dihydrofolate reductase enzymes. Biochem J 2018; 475:2107-2125. [PMID: 29871875 DOI: 10.1042/bcj20180249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 01/30/2023]
Abstract
Structural stability is a major constraint on the evolution of protein sequences. However, under strong directional selection, mutations that confer novel phenotypes but compromise structural stability of proteins may be permissible. During the evolution of antibiotic resistance, mutations that confer drug resistance often have pleiotropic effects on the structure and function of antibiotic-target proteins, usually essential metabolic enzymes. In the present study, we show that trimethoprim (TMP)-resistant alleles of dihydrofolate reductase from Escherichia coli (EcDHFR) harboring the Trp30Gly, Trp30Arg or Trp30Cys mutations are significantly less stable than the wild-type, making them prone to aggregation and proteolysis. This destabilization is associated with a lower expression level, resulting in a fitness cost and negative epistasis with other TMP-resistant mutations in EcDHFR. Using structure-based mutational analysis, we show that perturbation of critical stabilizing hydrophobic interactions in wild-type EcDHFR enzyme explains the phenotypes of Trp30 mutants. Surprisingly, though crucial for the stability of EcDHFR, significant sequence variation is found at this site among bacterial dihydrofolate reductases (DHFRs). Mutational and computational analyses in EcDHFR and in DHFR enzymes from Staphylococcus aureus and Mycobacterium tuberculosis demonstrate that natural variation at this site and its interacting hydrophobic residues modulates TMP resistance in other bacterial DHFRs as well, and may explain the different susceptibilities of bacterial pathogens to TMP. Our study demonstrates that trade-offs between structural stability and function can influence innate drug resistance as well as the potential for mutationally acquired drug resistance of an enzyme.
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81
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Zhang C, Samad M, Yu H, Chakroun N, Hilton D, Dalby PA. Computational Design To Reduce Conformational Flexibility and Aggregation Rates of an Antibody Fab Fragment. Mol Pharm 2018; 15:3079-3092. [PMID: 29897777 DOI: 10.1021/acs.molpharmaceut.8b00186] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computationally guided semirational design has significant potential for improving the aggregation kinetics of protein biopharmaceuticals. While improvement in the global conformational stability can stabilize proteins to aggregation under some conditions, previous studies suggest that such an approach is limited, because thermal transition temperatures ( Tm) and the fraction of protein unfolded ( fT) tend to only correlate with aggregation kinetics where the protein is incubated at temperatures approaching the Tm. This is because under these conditions, aggregation from globally unfolded protein becomes dominant. However, under native conditions, the aggregation kinetics are presumed to be dependent on local structural fluctuations or partial unfolding of the native state, which reveal regions of high propensity to form protein-protein interactions that lead to aggregation. In this work, we have targeted the design of stabilizing mutations to regions of the A33 Fab surface structure, which were predicted to be more flexible. This Fab already has high global stability, and global unfolding is not the main cause of aggregation under most conditions. Therefore, the aim was to reduce the conformational flexibility and entropy of the native protein at various locations and thus identify which of those regions has the greatest influence on the aggregation kinetics. Highly dynamic regions of structure were identified through both molecular dynamics simulation and B-factor analysis of related X-ray crystal structures. The most flexible residues were mutated into more stable variants, as predicted by Rosetta, which evaluates the ΔΔ GND for each potential point mutation. Additional destabilizing variants were prepared as controls to evaluate the prediction accuracy and also to assess the general influence of conformational stability on aggregation kinetics. The thermal conformational stability, and aggregation rates of 18 variants at 65 °C, were each examined at pH 4, 200 mM ionic strength, under which conditions the initial wild-type protein was <5% unfolded. Variants with decreased Tm values led to more rapid aggregation due to an increase in the fraction of protein unfolded under the conditions studied. As expected, no significant improvements were observed in the global conformational stability as measured by Tm. However, 6 of the 12 stable variants led to an increase in the cooperativity of unfolding, consistent with lower conformational flexibility and entropy in the native ensemble. Three of these had 5-11% lower aggregation rates, and their structural clustering indicated that the local dynamics of the C-terminus of the heavy chain had a role in influencing the aggregation rate.
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Affiliation(s)
- Cheng Zhang
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
| | - Maariyah Samad
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
| | - Haoran Yu
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
| | - Nesrine Chakroun
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
| | - David Hilton
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
| | - Paul A Dalby
- Department of Biochemical Engineering , University College London , Gordon Street , London WC1E 7JE , U.K
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82
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Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson BO. The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Front Microbiol 2018; 9:1082. [PMID: 29887846 PMCID: PMC5981134 DOI: 10.3389/fmicb.2018.01082] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/07/2018] [Indexed: 01/24/2023] Open
Abstract
Two-component systems (TCSs) consist of a histidine kinase and a response regulator. Here, we evaluated the conservation of the AgrAC TCS among 149 completely sequenced Staphylococcus aureus strains. It is composed of four genes: agrBDCA. We found that: (i) AgrAC system (agr) was found in all but one of the 149 strains, (ii) the agr positive strains were further classified into four agr types based on AgrD protein sequences, (iii) the four agr types not only specified the chromosomal arrangement of the agr genes but also the sequence divergence of AgrC histidine kinase protein, which confers signal specificity, (iv) the sequence divergence was reflected in distinct structural properties especially in the transmembrane region and second extracellular binding domain, and (v) there was a strong correlation between the agr type and the virulence genomic profile of the organism. Taken together, these results demonstrate that bioinformatic analysis of the agr locus leads to a classification system that correlates with the presence of virulence factors and protein structural properties.
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Affiliation(s)
- Kumari S Choudhary
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Nathan Mih
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Bioinformatics and Systems Biology Program, University of California, San Diego, San Diego, CA, United States
| | - Jonathan Monk
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Erol Kavvas
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - James T Yurkovich
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Bioinformatics and Systems Biology Program, University of California, San Diego, San Diego, CA, United States
| | - George Sakoulas
- Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
| | - Bernhard O Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Bioinformatics and Systems Biology Program, University of California, San Diego, San Diego, CA, United States.,Department of Pediatrics, University of California, San Diego, San Diego, CA, United States
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83
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Shanthirabalan S, Chomilier J, Carpentier M. Structural effects of point mutations in proteins. Proteins 2018; 86:853-867. [DOI: 10.1002/prot.25499] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 03/19/2018] [Accepted: 03/20/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Suvethigaa Shanthirabalan
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE; Paris France
| | | | - Mathilde Carpentier
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE; Paris France
- Sorbonne Université, CNRS, MNHN, IRD, IMPMC, BiBiP; Paris France
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84
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Davis CM, Gruebele M. Labeling for Quantitative Comparison of Imaging Measurements in Vitro and in Cells. Biochemistry 2018; 57:1929-1938. [PMID: 29546761 DOI: 10.1021/acs.biochem.8b00141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Qualitative imaging of biomolecular localization and distribution inside cells has revolutionized cell biology. Most of these powerful techniques require modifications to the target biomolecule. Over the past 10 years, these techniques have been extended to quantitative measurements, from in-cell protein folding rates to complex dissociation constants to RNA lifetimes. Such measurements can be affected even when a target molecule is just mildly perturbed by its labels. Here, the impact of labeling on protein (and RNA) structure, stability, and function in cells is discussed via practical examples from the recent literature. General guidelines for selecting and validating modification sites are provided to bring the best from cell biology and imaging to quantitative biophysical experiments inside cells.
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85
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Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations. Int J Mol Sci 2018; 19:ijms19030916. [PMID: 29558421 PMCID: PMC5877777 DOI: 10.3390/ijms19030916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/15/2018] [Accepted: 03/17/2018] [Indexed: 12/17/2022] Open
Abstract
A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm. The differentiated pathways for the six core residues form a dynamic network that outlines the area of structure alteration. The results offer potentials of using affordable computing power to predict allosteric structure of mutants in knowledge-based mutagenesis.
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86
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Vanacek P, Sebestova E, Babkova P, Bidmanova S, Daniel L, Dvorak P, Stepankova V, Chaloupkova R, Brezovsky J, Prokop Z, Damborsky J. Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03523] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Pavel Vanacek
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Eva Sebestova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Petra Babkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Sarka Bidmanova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Lukas Daniel
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Pavel Dvorak
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Veronika Stepankova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis
Ltd., Biotechnology Incubator INBIT, Kamenice 34, 625 00 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis
Ltd., Biotechnology Incubator INBIT, Kamenice 34, 625 00 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis
Ltd., Biotechnology Incubator INBIT, Kamenice 34, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
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87
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Hoernes TP, Clementi N, Juen MA, Shi X, Faserl K, Willi J, Gasser C, Kreutz C, Joseph S, Lindner H, Hüttenhofer A, Erlacher MD. Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor-mediated peptide release. Proc Natl Acad Sci U S A 2018; 115:E382-E389. [PMID: 29298914 PMCID: PMC5776981 DOI: 10.1073/pnas.1714554115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Termination of protein synthesis is triggered by the recognition of a stop codon at the ribosomal A site and is mediated by class I release factors (RFs). Whereas in bacteria, RF1 and RF2 promote termination at UAA/UAG and UAA/UGA stop codons, respectively, eukaryotes only depend on one RF (eRF1) to initiate peptide release at all three stop codons. Based on several structural as well as biochemical studies, interactions between mRNA, tRNA, and rRNA have been proposed to be required for stop codon recognition. In this study, the influence of these interactions was investigated by using chemically modified stop codons. Single functional groups within stop codon nucleotides were substituted to weaken or completely eliminate specific interactions between the respective mRNA and RFs. Our findings provide detailed insight into the recognition mode of bacterial and eukaryotic RFs, thereby revealing the chemical groups of nucleotides that define the identity of stop codons and provide the means to discriminate against noncognate stop codons or UGG sense codons.
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Affiliation(s)
- Thomas Philipp Hoernes
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Clementi
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Michael Andreas Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Xinying Shi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314
| | - Klaus Faserl
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Jessica Willi
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Catherina Gasser
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, 6020 Innsbruck, Austria
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0314
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Alexander Hüttenhofer
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Matthias David Erlacher
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria;
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88
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Tiberti M, Pandini A, Fraternali F, Fornili A. In silico identification of rescue sites by double force scanning. Bioinformatics 2018; 34:207-214. [PMID: 28961796 PMCID: PMC5860198 DOI: 10.1093/bioinformatics/btx515] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/23/2017] [Accepted: 08/10/2017] [Indexed: 01/03/2023] Open
Abstract
Motivation A deleterious amino acid change in a protein can be compensated by a second-site rescue mutation. These compensatory mechanisms can be mimicked by drugs. In particular, the location of rescue mutations can be used to identify protein regions that can be targeted by small molecules to reactivate a damaged mutant. Results We present the first general computational method to detect rescue sites. By mimicking the effect of mutations through the application of forces, the double force scanning (DFS) method identifies the second-site residues that make the protein structure most resilient to the effect of pathogenic mutations. We tested DFS predictions against two datasets containing experimentally validated and putative evolutionary-related rescue sites. A remarkably good agreement was found between predictions and experimental data. Indeed, almost half of the rescue sites in p53 was correctly predicted by DFS, with 65% of remaining sites in contact with DFS predictions. Similar results were found for other proteins in the evolutionary dataset. Availability and implementation The DFS code is available under GPL at https://fornililab.github.io/dfs/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matteo Tiberti
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Alessandro Pandini
- Department of Computer Science, College of Engineering, Design and Physical Sciences and Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, London, UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King‘s College London, London, UK
- The Francis Crick Institute, London, UK
- The Thomas Young Centre for Theory and Simulation of Materials, London, UK
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- The Thomas Young Centre for Theory and Simulation of Materials, London, UK
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89
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Rossier BC, Bochud M, Devuyst O. The Hypertension Pandemic: An Evolutionary Perspective. Physiology (Bethesda) 2017; 32:112-125. [PMID: 28202622 DOI: 10.1152/physiol.00026.2016] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hypertension affects over 1.2 billion individuals worldwide and has become the most critical and expensive public health problem. Hypertension is a multifactorial disease involving environmental and genetic factors together with risk-conferring behaviors. The cause of the disease is identified in ∼10% of the cases (secondary hypertension), but in 90% of the cases no etiology is found (primary or essential hypertension). For this reason, a better understanding of the mechanisms controlling blood pressure in normal and hypertensive patients is the aim of very active experimental and clinical research. In this article, we review the importance of the renin-angiotensin-aldosterone system (RAAS) for the control of blood pressure, focusing on the evolution of the system and its critical importance for adaptation of vertebrates to a terrestrial and dry environment. The evolution of blood pressure control during the evolution of primates, hominins, and humans is discussed, together with the role of common genetic factors and the possible causes of the current hypertension pandemic in the light of evolutionary medicine.
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Affiliation(s)
- Bernard C Rossier
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland;
| | - Murielle Bochud
- Institute of Social and Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland; and
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland
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90
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Völler JS, Thi To TM, Biava H, Koksch B, Budisa N. Global substitution of hemeproteins with noncanonical amino acids in Escherichia coli with intact cofactor maturation machinery. Enzyme Microb Technol 2017; 106:55-59. [PMID: 28859810 DOI: 10.1016/j.enzmictec.2017.06.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/19/2022]
Abstract
Global substitution of canonical amino acids (cAAs) with noncanonical (ncAAs) counterparts in proteins whose function is dependent on post-translational events such as cofactor binding is still a methodically challenging and difficult task as ncAA insertion generally interferes with the cofactor biosynthesis machinery. Here, we report a technology for the expression of fully substituted and functionally active cofactor-containing hemeproteins. The maturation process which yields an intact cofactor is timely separated from cAA→ncAA substitutions. This is achieved by an optimised expression and fermentation procedure which includes pre-induction of the heme cofactor biosynthesis followed by an incorporation experiment at multiple positions in the protein sequence. This simple strategy can be potentially applied for engineering of other cofactor-containing enzymes.
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Affiliation(s)
- Jan-Stefan Völler
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany; Institute of Chemistry and Biochemistry - Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Tuyet Mai Thi To
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany; Institute of Chemistry and Biochemistry - Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Hernan Biava
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry - Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Nediljko Budisa
- Department of Chemistry, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany.
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91
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Associations of ERAP1 coding variants and domain specific interaction with HLA-C∗06 in the early onset psoriasis patients of India. Hum Immunol 2017; 78:724-730. [PMID: 28867178 DOI: 10.1016/j.humimm.2017.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/20/2017] [Accepted: 08/29/2017] [Indexed: 11/23/2022]
Abstract
Interferon-γ-induced aminopeptidase ERAP1 trims peptides within the endoplasmic reticulum so that they can be loaded onto MHC class I and presented to the CD8+ T-cells. ERAP1 association and its interaction with HLA-C∗06 is controversial across different populations. We have investigated the association and possible functional role of non-synonymous SNPs at different exons of ERAP1 (rs26653: Arg127Pro, rs30187: Lys528Arg and rs27044: Gln730Glu) and their interactions with HLA-C∗06 in psoriasis. Significant associations of HLA-C∗06 (OR=5.47, P<2.2×10-16), rs30187 (OR 1.35, P=7.4×10-4) and rs27044 (OR=1.24, P=5.8×10-3) were observed. All three ERAP1 SNPs showed significant association only for HLA-C∗06 positive patients, while rs30187 and rs27044 showed significant association only for early onset patients (rs30187: OR=1.47, P=9.6×10-5; rs27044: OR=1.36, P=3.3×10-4). No differential expression of ERAP1 was observed either between paired uninvolved and involved skin tissues of psoriasis patients or between non-risk and risk variants in the involved skin. Significant epistatic interaction was observed between HLA-C∗06 and the SNP (rs27044) located at the peptide-binding cavity of ERAP1. Evolutionary conservation analysis among mammals showed confinement of Lys528 and Gln730 within highly conserved regions of ERAP1 and suggested the possible detrimental effect of this allele in ERAP1 regulation.
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92
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Lin M, Whitmire S, Chen J, Farrel A, Shi X, Guo JT. Effects of short indels on protein structure and function in human genomes. Sci Rep 2017; 7:9313. [PMID: 28839204 PMCID: PMC5570956 DOI: 10.1038/s41598-017-09287-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/24/2017] [Indexed: 01/20/2023] Open
Abstract
Insertions and deletions (indels) represent the second most common type of genetic variations in human genomes. Indels can be deleterious and contribute to disease susceptibility as recent genome sequencing projects revealed a large number of indels in various cancer types. In this study, we investigated the possible effects of small coding indels on protein structure and function, and the baseline characteristics of indels in 2504 individuals of 26 populations from the 1000 Genomes Project. We found that each population has a distinct pattern in genes with small indels. Frameshift (FS) indels are enriched in olfactory receptor activity while non-frameshift (NFS) indels are enriched in transcription-related proteins. Structural analysis of NFS indels revealed that they predominantly adopt coil or disordered conformations, especially in proteins with transcription-related NFS indels. These results suggest that the annotated coding indels from the 1000 Genomes Project, while contributing to genetic variations and phenotypic diversity, generally do not affect the core protein structures and have no deleterious effect on essential biological processes. In addition, we found that a number of reference genome annotations might need to be updated due to the high prevalence of annotated homozygous indels in the general population.
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Affiliation(s)
- Maoxuan Lin
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Sarah Whitmire
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jing Chen
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Alvin Farrel
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Xinghua Shi
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jun-Tao Guo
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
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93
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Martins L, Giovani PA, Rebouças PD, Brasil DM, Haiter Neto F, Coletta RD, Machado RA, Puppin-Rontani RM, Nociti FH, Kantovitz KR. Computational analysis for GNAQ mutations: New insights on the molecular etiology of Sturge-Weber syndrome. J Mol Graph Model 2017; 76:429-440. [PMID: 28779688 DOI: 10.1016/j.jmgm.2017.07.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 12/13/2022]
Abstract
Somatic activating mutations in the GNAQ have been recently associated with several congenital genetic disorders and tumors; however, the molecular mechanism/etiology that leads to GNAQ somatic mosaic mutation are unknown. Here, we reported a case of Sturge-Weber Syndrome (SWS) manifesting cutaneous vascular malformations (hemifacial Port-wine stain), cerebral and ocular vascular abnormalities (including epilepsy and glaucoma) and harboring a c.548G>A (p.R183Q) somatic mosaic mutation in GNAQ. Computational modeling studies were performed to assistant with the comprehension of the functional impact of p.R183Q and p.Q209L mutations in GNAQ, which encodes a G protein subunit alpha q (Gαq). The p.R183Q mutation was predicted to abolish hydrogen bonds between R183 residue and GDP molecule, destabilizing the inactive GDP-bound conformation of the Gαq mutants. Furthermore, replacement of R183 by Q183 residue was predicted to promote conformation changes in protein surface features affecting the switch I region, a key region that undergoes conformational changes triggered by receptor binding during signal transduction. In addition, replacement of Q209 by L209 residue was predicted to affect the molecular interaction between Gαq and Gβ subunit, impairing formation of the inactive heterotrimeric complex. These findings, in association with PPI network analysis, indicate that p.R183Q and p.Q209L mutations result in the over-activation of different downstream effectors, which in turn will determine the distinct cell responses and phenotype. These findings bring new insights on molecular etiology of vascular malformations associated to SWS and on different mechanisms underlying hyperactivation of downstream pathways to Gαq.
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Affiliation(s)
- Luciane Martins
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Priscila Alves Giovani
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Pedro Diniz Rebouças
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Danieli Moura Brasil
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Francisco Haiter Neto
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Renato Assis Machado
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Regina Maria Puppin-Rontani
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Francisco Humberto Nociti
- Department of Prosthodontics and Periodontics, Division of Periodontics, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil
| | - Kamila Rosamilia Kantovitz
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, SP, Brazil; Department of Dental Materials, São Leopoldo Mandic School of Dentistry and Research Center, Campinas, SP, Brazil.
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94
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Nagamune T. Biomolecular engineering for nanobio/bionanotechnology. NANO CONVERGENCE 2017; 4:9. [PMID: 28491487 PMCID: PMC5401866 DOI: 10.1186/s40580-017-0103-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/29/2017] [Indexed: 05/02/2023]
Abstract
Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.
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Affiliation(s)
- Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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95
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P. S, D. TK, C. GPD, R. S, Zayed H. Determining the role of missense mutations in the POU domain of HNF1A that reduce the DNA-binding affinity: A computational approach. PLoS One 2017; 12:e0174953. [PMID: 28410371 PMCID: PMC5391926 DOI: 10.1371/journal.pone.0174953] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/18/2017] [Indexed: 12/21/2022] Open
Abstract
Maturity-onset diabetes of the young type 3 (MODY3) is a non-ketotic form of diabetes associated with poor insulin secretion. Over the past years, several studies have reported the association of missense mutations in the Hepatocyte Nuclear Factor 1 Alpha (HNF1A) with MODY3. Missense mutations in the POU homeodomain (POUH) of HNF1A hinder binding to the DNA, thereby leading to a dysfunctional protein. Missense mutations of the HNF1A were retrieved from public databases and subjected to a three-step computational mutational analysis to identify the underlying mechanism. First, the pathogenicity and stability of the mutations were analyzed to determine whether they alter protein structure and function. Second, the sequence conservation and DNA-binding sites of the mutant positions were assessed; as HNF1A protein is a transcription factor. Finally, the biochemical properties of the biological system were validated using molecular dynamic simulations in Gromacs 4.6.3 package. Two arginine residues (131 and 203) in the HNF1A protein are highly conserved residues and contribute to the function of the protein. Furthermore, the R131W, R131Q, and R203C mutations were predicted to be highly deleterious by in silico tools and showed lower binding affinity with DNA when compared to the native protein using the molecular docking analysis. Triplicate runs of molecular dynamic (MD) simulations (50ns) revealed smaller changes in patterns of deviation, fluctuation, and compactness, in complexes containing the R131Q and R131W mutations, compared to complexes containing the R203C mutant complex. We observed reduction in the number of intermolecular hydrogen bonds, compactness, and electrostatic potential, as well as the loss of salt bridges, in the R203C mutant complex. Substitution of arginine with cysteine at position 203 decreases the affinity of the protein for DNA, thereby destabilizing the protein. Based on our current findings, the MD approach is an important tool for elucidating the impact and affinity of mutations in DNA-protein interactions and understanding their function.
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Affiliation(s)
- Sneha P.
- School of BioSciences and Technology,Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Thirumal Kumar D.
- School of BioSciences and Technology,Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - George Priya Doss C.
- School of BioSciences and Technology,Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Siva R.
- School of BioSciences and Technology,Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
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96
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Molecular Evolutionary Constraints that Determine the Avirulence State of Clostridium botulinum C2 Toxin. J Mol Evol 2017; 84:174-186. [DOI: 10.1007/s00239-017-9791-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 03/30/2017] [Indexed: 10/19/2022]
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97
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Ball C, Awad F, Hutton S, Forrester A, Baylis M, Ganapathy K. Infectious bronchitis vaccine virus detection and part-S1 genetic variation following single or dual inoculation in broiler chicks. Avian Pathol 2017; 46:309-318. [PMID: 27917677 DOI: 10.1080/03079457.2016.1268675] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An investigation was undertaken of the extent of genetic variation occurring within infectious bronchitis virus (IBV) vaccine strains following vaccination of day-old broiler chicks. Chicks were divided into seven groups, with two groups receiving single Massachusetts (Mass) vaccinations while the other four were inoculated with combinations of different IBV serotypes; Mass, 793B, D274 and Arkansas (Ark). The remaining group was maintained as an unvaccinated control. Following vaccination, swabs and tissues collected at intervals were pooled and RNA was extracted for detection of IBV by reverse transcription polymerase chain reaction. Positive amplicons were sequenced for the part-S1 gene and compared to the original vaccine strain sequences. Single nucleotide polymorphisms, amino acid variations and hydrophobicity changes were identified and recorded for each sampling point. A total of 106 single nucleotide polymorphisms were detected within 28 isolates. The average single nucleotide polymorphism counts of swab isolates were greater than those found in tissue samples. This translated into 64 amino acid changes; however only six resulted in a change to the hydrophobicity properties. All hydrophobic alterations occurred within swab isolates and the majority were recovered at 3 days post vaccination suggesting such changes to be detrimental to early virus survival. Nucleotide deletions were seen only in the group given the combination of Mass and Ark. Of the 16 sequenced samples in this group, 13 contained the same AAT deletion at position 1033 1035 in the Ark strains. Findings presented in this study demonstrate alteration in the S1 nucleotide sequence following co-administration of live IBV vaccines.
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Affiliation(s)
- Christopher Ball
- a Institute of Infection and Global Health, University of Liverpool, Leahurst Campus , Cheshire , UK
| | - Faez Awad
- a Institute of Infection and Global Health, University of Liverpool, Leahurst Campus , Cheshire , UK.,b Faculty of Veterinary Medicine , University of Omar Al-Mukhtar , Al-Bayda , Libya
| | - Sally Hutton
- a Institute of Infection and Global Health, University of Liverpool, Leahurst Campus , Cheshire , UK
| | - Anne Forrester
- a Institute of Infection and Global Health, University of Liverpool, Leahurst Campus , Cheshire , UK
| | - Matthew Baylis
- a Institute of Infection and Global Health, University of Liverpool, Leahurst Campus , Cheshire , UK.,c NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool , Liverpool , UK
| | - Kannan Ganapathy
- a Institute of Infection and Global Health, University of Liverpool, Leahurst Campus , Cheshire , UK
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98
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Nitsche C, Mahawaththa MC, Becker W, Huber T, Otting G. Site-selective tagging of proteins by pnictogen-mediated self-assembly. Chem Commun (Camb) 2017; 53:10894-10897. [DOI: 10.1039/c7cc06155b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Trivalent pnictogens (Pn) enable the selective self-assembly between an engineered di-cysteine motif in a protein and a thiol-containing lanthanide (Ln) probe.
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Affiliation(s)
- Christoph Nitsche
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | | | - Walter Becker
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Thomas Huber
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Gottfried Otting
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
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99
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Lathrop BK. Biophysical Evidence Relevant to the Patentability of Engineered Antibodies: Using Computational Simulations to Assist the Objective Analysis Required by Section § 112(a). Biotechnol Law Rep 2016. [DOI: 10.1089/blr.2016.29024.bkl] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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100
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Saw SH, Tan JL, Chan XY, Chan KG, Ngeow YF. Chromosomal rearrangements and protein globularity changes in Mycobacterium tuberculosis isolates from cerebrospinal fluid. PeerJ 2016; 4:e2484. [PMID: 27688977 PMCID: PMC5036109 DOI: 10.7717/peerj.2484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 08/24/2016] [Indexed: 01/07/2023] Open
Abstract
Background Meningitis is a major cause of mortality in tuberculosis (TB). It is not clear what factors promote central nervous system invasion and pathology but it has been reported that certain strains of Mycobacterium tuberculosis (Mtb) might have genetic traits associated with neurotropism. Methods In this study, we generated whole genome sequences of eight clinical strains of Mtb that were isolated from the cerebrospinal fluid (CSF) of patients presenting with tuberculous meningitis (TBM) in Malaysia, and compared them to the genomes of H37Rv and other respiratory Mtb genomes either downloaded from public databases or extracted from local sputum isolates. We aimed to find genomic features that might be distinctly different between CSF-derived and respiratory Mtb. Results Genome-wide comparisons revealed rearrangements (translocations, inversions, insertions and deletions) and non-synonymous SNPs in our CSF-derived strains that were not observed in the respiratory Mtb genomes used for comparison. These rearranged segments were rich in genes for PE (proline-glutamate)/PPE (proline-proline-glutamate), transcriptional and membrane proteins. Similarly, most of the ns SNPs common in CSF strains were noted in genes encoding PE/PPE proteins. Protein globularity differences were observed among mycobacteria from CSF and respiratory sources and in proteins previously reported to be associated with TB meningitis. Transcription factors and other transcription regulators featured prominently in these proteins. Homologs of proteins associated with Streptococcus pneumoniae meningitis and Neisseria meningitidis virulence were identified in neuropathogenic as well as respiratory mycobacterial spp. examined in this study. Discussion The occurrence of in silico genetic differences in CSF-derived but not respiratory Mtb suggests their possible involvement in the pathogenesis of TBM. However, overall findings in this comparative analysis support the postulation that TB meningeal infection is more likely to be related to the expression of multiple virulence factors on interaction with host defences than to CNS tropism associated with specific genetic traits.
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Affiliation(s)
- Seow Hoon Saw
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Malaysia.,Department of Biomedical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar, Perak, Malaysia
| | - Joon Liang Tan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.,Faculty of Information Science and Technology, Multimedia University, Melaka, Malaysia
| | - Xin Yue Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Yun Fong Ngeow
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Bandar Sungai Long, Malaysia.,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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