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Azzeri A, Mohamed NA, Wan Rosli SH, Abdul Samat MN, Rashid ZZ, Mohamad Jamali MA, Md Zoqratt MZH, Mohammad Nasir MA, Ranjit Singh HK, Azmi L. Unravelling the link between SARS-CoV-2 mutation frequencies, patient comorbidities, and structural dynamics. PLoS One 2024; 19:e0291892. [PMID: 38483913 PMCID: PMC10939192 DOI: 10.1371/journal.pone.0291892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Genomic surveillance is crucial for tracking emergence and spread of novel variants of pathogens, such as SARS-CoV-2, to inform public health interventions and to enforce control measures. However, in some settings especially in low- and middle- income counties, where sequencing platforms are limited, only certain patients get to be selected for sequencing surveillance. Here, we show that patients with multiple comorbidities potentially harbour SARS-CoV-2 with higher mutation rates and thus deserve more attention for genomic surveillance. The relationship between the patient comorbidities, and type of amino acid mutations was assessed. Correlation analysis showed that there was a significant tendency for mutations to occur within the ORF1a region for patients with higher number of comorbidities. Frequency analysis of the amino acid substitution within ORF1a showed that nsp3 P822L of the PLpro protease was one of the highest occurring mutations. Using molecular dynamics, we simulated that the P822L mutation in PLpro represents a system with lower Root Mean Square Deviation (RMSD) fluctuations, and consistent Radius of gyration (Rg), Solvent Accessible Surface Area (SASA) values-indicate a much stabler protein than the wildtype. The outcome of this study will help determine the relationship between the clinical status of a patient and the mutations of the infecting SARS-CoV-2 virus.
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Affiliation(s)
- Amirah Azzeri
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Negeri Sembilan, Malaysia
| | - Nurul Azmawati Mohamed
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Negeri Sembilan, Malaysia
| | - Saarah Huurieyah Wan Rosli
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Negeri Sembilan, Malaysia
| | - Muttaqillah Najihan Abdul Samat
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | - Zetti Zainol Rashid
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | | | - Muhammad Zarul Hanifah Md Zoqratt
- Fast Genomics Solutions, Subang Jaya, Selangor Darul Ehsan, Malaysia
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Muhammad Azamuddeen Mohammad Nasir
- Fast Genomics Solutions, Subang Jaya, Selangor Darul Ehsan, Malaysia
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Harpreet Kaur Ranjit Singh
- Fast Genomics Solutions, Subang Jaya, Selangor Darul Ehsan, Malaysia
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Liyana Azmi
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Negeri Sembilan, Malaysia
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Juliana N, Azmi L, Effendy NM, Mohd Fahmi Teng NI, Abu IF, Abu Bakar NN, Azmani S, Yazit NAA, Kadiman S, Das S. Effect of Circadian Rhythm Disturbance on the Human Musculoskeletal System and the Importance of Nutritional Strategies. Nutrients 2023; 15:nu15030734. [PMID: 36771440 PMCID: PMC9920183 DOI: 10.3390/nu15030734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
The circadian system in the human body responds to daily environmental changes to optimise behaviour according to the biological clock and also influences various physiological processes. The suprachiasmatic nuclei are located in the anterior hypothalamus of the brain, and they synchronise to the 24 h light/dark cycle. Human physiological functions are highly dependent on the regulation of the internal circadian clock. Skeletal muscles comprise the largest collection of peripheral clocks in the human body. Both central and peripheral clocks regulate the interaction between the musculoskeletal system and energy metabolism. The skeletal muscle circadian clock plays a vital role in lipid and glucose metabolism. The pathogenesis of osteoporosis is related to an alteration in the circadian rhythm. In the present review, we discuss the disturbance of the circadian rhythm and its resultant effect on the musculoskeletal system. We also discuss the nutritional strategies that are potentially effective in maintaining the system's homeostasis. Active collaborations between nutritionists and physiologists in the field of chronobiological and chrononutrition will further clarify these interactions. This review may be necessary for successful interventions in reducing morbidity and mortality resulting from musculoskeletal disturbances.
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Affiliation(s)
- Norsham Juliana
- Faculty Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Malaysia
- Correspondence: ; Tel.: +60-13-331-1706
| | - Liyana Azmi
- Faculty Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Malaysia
| | - Nadia Mohd Effendy
- Faculty Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Malaysia
| | | | - Izuddin Fahmy Abu
- Institute of Medical Science Technology, Universiti Kuala Lumpur, Kajang 43000, Malaysia
| | - Nur Nabilah Abu Bakar
- Faculty Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Malaysia
| | - Sahar Azmani
- Faculty Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Malaysia
| | - Noor Anisah Abu Yazit
- Faculty Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai 71800, Malaysia
| | - Suhaini Kadiman
- Anaesthesia and Intensive Care Unit, National Heart Institute, Kuala Lumpur 50400, Malaysia
| | - Srijit Das
- Department of Human & Clinical Anatomy, College of Medicine & Health Sciences, Sultan Qaboos University, Al-Khoud, Muscat 123, Oman
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Azmi L, Bragginton EC, Cadby IT, Byron O, Roe AJ, Lovering AL, Gabrielsen M. High-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE. Acta Crystallogr F Struct Biol Commun 2020; 76:414-421. [PMID: 32880589 PMCID: PMC7470043 DOI: 10.1107/s2053230x20010237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/23/2020] [Indexed: 11/13/2023] Open
Abstract
The bifunctional alcohol/aldehyde dehydrogenase (AdhE) comprises both an N-terminal aldehyde dehydrogenase (AldDH) and a C-terminal alcohol dehydrogenase (ADH). In vivo, full-length AdhE oligomerizes into long oligomers known as spirosomes. However, structural analysis of AdhE is challenging owing to the heterogeneity of the spirosomes. Therefore, the domains of AdhE are best characterized separately. Here, the structure of ADH from the pathogenic Escherichia coli O157:H7 was determined to 1.65 Å resolution. The dimeric crystal structure was confirmed in solution by small-angle X-ray scattering.
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Affiliation(s)
- Liyana Azmi
- Institute of Infection, Immunity and Inflammation, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Eilis C Bragginton
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Ian T Cadby
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Olwyn Byron
- Institute of Infection, Immunity and Inflammation, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Andrew L Lovering
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Mads Gabrielsen
- CRUK Beatson Institute, Switchback Road, Glasgow G61 1BD, United Kingdom
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Kim G, Azmi L, Jang S, Jung T, Hebert H, Roe AJ, Byron O, Song JJ. Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity. Nat Commun 2019; 10:4527. [PMID: 31586059 PMCID: PMC6778083 DOI: 10.1038/s41467-019-12427-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023] Open
Abstract
Aldehyde-alcohol dehydrogenase (AdhE) is a key enzyme in bacterial fermentation, converting acetyl-CoA to ethanol, via two consecutive catalytic reactions. Here, we present a 3.5 Å resolution cryo-EM structure of full-length AdhE revealing a high-order spirosome architecture. The structure shows that the aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) active sites reside at the outer surface and the inner surface of the spirosome respectively, thus topologically separating these two activities. Furthermore, mutations disrupting the helical structure abrogate enzymatic activity, implying that formation of the spirosome structure is critical for AdhE activity. In addition, we show that this spirosome structure undergoes conformational change in the presence of cofactors. This work presents the atomic resolution structure of AdhE and suggests that the high-order helical structure regulates its enzymatic activity. Aldehyde-alcohol dehydrogenase (AdhE) converts acetyl-CoA to ethanol and plays an important role in bacterial fermentation. Here the authors present the 3.5 Å cryo-EM structure of full-length E. coli AdhE, which reveals a right-handed helical spirosome structure and they show that the helical structure is required for AdhE activity.
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Affiliation(s)
- Gijeong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Liyana Azmi
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Seongmin Jang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Taeyang Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.,School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Novum, SE-141 57, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83, Huddinge, Sweden
| | - Hans Hebert
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Novum, SE-141 57, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83, Huddinge, Sweden
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.
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Azmi L, Shukla I, Kant P, Rao C. 1-hydroxy-5, 7-dimethoxy-2 naphthalene-carboxaldehyde inhibitors as novel antimycobacterial agents targeting H-InMyoFib cells and targeting enzymes involved in fatty acid biosynthesis of bacilli. Int J Infect Dis 2018. [DOI: 10.1016/j.ijid.2018.04.3622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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