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Gupta SK, Banerjee S, Prabhakaran EN. Understanding the anomaly of cis-trans isomerism in Pro-His sequence. Bioorg Med Chem Lett 2022; 76:128985. [PMID: 36165914 DOI: 10.1016/j.bmcl.2022.128985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/05/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022]
Abstract
The anomalous absence of cisPro stabilizing CαHαXaa···πAro interactions at Xaa-Pro-Aro exclusively when Aro is His, is understood by NMR structural analyses of model peptides, as due to i → i backbone-side chain C6 H-bond that forms uniquely when Aro is His, which significantly decreases its χ1-g- population essential for CαHαXaa···πAro formation.
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Affiliation(s)
- Sunil K Gupta
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Shreya Banerjee
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Erode N Prabhakaran
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India.
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2
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Perera DDBD, Perera KML, Peiris DC. A Novel In Silico Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery. BIOLOGY 2021; 10:biology10111113. [PMID: 34827106 PMCID: PMC8615085 DOI: 10.3390/biology10111113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/16/2021] [Accepted: 10/25/2021] [Indexed: 01/11/2023]
Abstract
Simple Summary Protein interactions govern the majority of an organism’s biological processes. Therefore, to fully understand the functionality of an organism, we must know how proteins work at a molecular level. This study assembled a protocol that enables scientists to construct a protein’s tertiary structure easily and subsequently to investigate its mechanism and function. Each step involved in prediction, validation, and functional analysis of a protein is crucial to obtain an accurate result. We have dubbed this the trifecta analysis. It was clear early in our research that no single study in the literature had previously encompassed the complete trifecta analysis. In particular, studies that recommend free, open-source tools that have been benchmarked for each step are lacking. The present study ensures that predictions are accurate and validated and will greatly benefit new and experienced scientists alike in obtaining a strong understanding of the trifecta analysis, resulting in a domino effect that could lead to drug development. Abstract Current in silico proteomics require the trifecta analysis, namely, prediction, validation, and functional assessment of a modeled protein. The main drawback of this endeavor is the lack of a single protocol that utilizes a proper set of benchmarked open-source tools to predict a protein’s structure and function accurately. The present study rectifies this drawback through the design and development of such a protocol. The protocol begins with the characterization of a novel coding sequence to identify the expressed protein. It then recognizes and isolates evolutionarily conserved sequence motifs through phylogenetics. The next step is to predict the protein’s secondary structure, followed by the prediction, refinement, and validation of its three-dimensional tertiary structure. These steps enable the functional analysis of the macromolecule through protein docking, which facilitates the identification of the protein’s active site. Each of these steps is crucial for the complete characterization of the protein under study. We have dubbed this process the trifecta analysis. In this study, we have proven the effectiveness of our protocol using the cystatin C and AChE proteins. Beginning with just their sequences, we have characterized both proteins’ structures and functions, including identifying the cystatin C protein’s seven-residue active site and the AChE protein’s active-site gorge via protein–protein and protein–ligand docking, respectively. This process will greatly benefit new and experienced scientists alike in obtaining a strong understanding of the trifecta analysis, resulting in a domino effect that could expand drug development.
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Affiliation(s)
- D. D. B. D. Perera
- Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka;
- Correspondence: (D.D.B.D.P.); (D.C.P.); Tel.: +94-714-018-537 (D.C.P.)
| | - K. Minoli L. Perera
- Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka;
| | - Dinithi C. Peiris
- Genetics & Molecular Biology Unit (Center for Biotechnology), Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka
- Correspondence: (D.D.B.D.P.); (D.C.P.); Tel.: +94-714-018-537 (D.C.P.)
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3
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Hua X, Wang Z, Wang Z, Chen L, Zhou Z, Ouyang J, Deng K, Yang X, Huang H. De Novo Development of a Universal Biosensing Platform by Rapid Direct Native Protein Modification. Anal Chem 2021; 93:5291-5300. [PMID: 33734672 DOI: 10.1021/acs.analchem.1c00341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An innovative biosensing assay was developed for simplified, cost-effective, and sensitive detection. By rapid, direct treatment of target proteins with iron porphyrin (TPPFe) in situ, a carboxyl group of amino acid conjugates with an Fe atom of the TPPFe molecule, forming a stable protein complex. We have shown that this complex not only maintains the integrity and functions of original proteins but also acquires peroxidase activity that can turn TMB to a comparably visible signal like that in ELISA. This study is unique since such conversion is difficult to achieve with standard chemical modification or molecular biology methods. In addition, the proposed immunoassay is superior to traditional ELISA as it eliminates an expensive and complicated cross-linking process of an enzyme-labeled antibody. From a practical point of view, we extended this assay to rapid detection of clinically relevant proteins and glucose in blood samples. The results show that this simple immunoassay provides clinical diagnosis, food safety, and environmental monitoring in an easy-to-implement manner.
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Affiliation(s)
- Xinyi Hua
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, China.,Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Zhifang Wang
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, China.,Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Ziqi Wang
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, China.,Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Linlin Chen
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, China.,Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Zaichun Zhou
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, China.,Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Junlin Ouyang
- School of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Keqin Deng
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, China.,Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Xiumei Yang
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, China.,Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
| | - Haowen Huang
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, China.,Hunan Provincial Key Laboratory of Controllable Preparation and Functional Application of Fine Polymers, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
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Shandilya M, Kumar G, Gomkale R, Singh S, Khan MA, Kateriya S, Kundu S. Multiple putative methemoglobin reductases in C. reinhardtii may support enzymatic functions for its multiple hemoglobins. Int J Biol Macromol 2021; 171:465-479. [PMID: 33428952 DOI: 10.1016/j.ijbiomac.2021.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/26/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
The ubiquitous nature of hemoglobins, their presence in multiple forms and low cellular expression in organisms suggests alternative physiological functions of hemoglobins in addition to oxygen transport and storage. Previous research has proposed enzymatic function of hemoglobins such as nitric oxide dioxygenase, nitrite reductase and hydroxylamine reductase. In all these enzymatic functions, active ferrous form of hemoglobin is converted to ferric form and reconversion of ferric to ferrous through reduction partners is under active investigation. The model alga C. reinhardtii contains multiple globins and is thus expected to have multiple putative methemoglobin reductases to augment the physiological functions of the novel hemoglobins. In this regard, three putative methemoglobin reductases and three algal hemoglobins were characterized. Our results signify that the identified putative methemoglobin reductases can reduce algal methemoglobins in a nonspecific manner under in vitro conditions. Enzyme kinetics of two putative methemoglobin reductases with methemoglobins as substrates and in silico analysis support interaction between the hemoglobins and the two reduction partners as also observed in vitro. Our investigation on algal methemoglobin reductases underpins the valuable chemistry of nitric oxide with the newly discovered hemoglobins to ensure their physiological relevance, with multiple hemoglobins probably necessitating the presence of multiple reductases.
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Affiliation(s)
- Manish Shandilya
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India; Amity School of Applied Sciences, Amity University Haryana, Gurugram 122413, India
| | - Gaurav Kumar
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Ridhima Gomkale
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Swati Singh
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Mohd Asim Khan
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India
| | - Suneel Kateriya
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India.
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Nye DB, Johnson EA, Mai MH, Lecomte JTJ. Replacement of the heme axial lysine as a test of conformational adaptability in the truncated hemoglobin THB1. J Inorg Biochem 2019; 201:110824. [PMID: 31514090 DOI: 10.1016/j.jinorgbio.2019.110824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/03/2019] [Accepted: 09/03/2019] [Indexed: 10/26/2022]
Abstract
Amino acid replacement is a useful strategy to assess the roles of axial heme ligands in the function of native heme proteins. THB1, the protein product of the Chlamydomonas reinhardtii THB1 gene, is a group 1 truncated hemoglobin that uses a lysine residue in the E helix (Lys53, at position E10 by reference to myoglobin) as an iron ligand at neutral pH. Phylogenetic evidence shows that many homologous proteins have a histidine, methionine or arginine at the same position. In THB1, these amino acids would each be expected to convey distinct reactive properties if replacing the native lysine as an axial ligand. To explore the ability of the group 1 truncated Hb fold to support alternative ligation schemes and distal pocket conformations, the properties of the THB1 variants K53A as a control, K53H, K53M, and K53R were investigated by electronic absorption, EPR, and NMR spectroscopies. We found that His53 is capable of heme ligation in both the Fe(III) and Fe(II) states, that Met53 can coordinate only in the Fe(II) state, and that Arg53 stabilizes a hydroxide ligand in the Fe(III) state. The data illustrate that the group 1 truncated Hb fold can tolerate diverse rearrangement of the heme environment and has a strong tendency to use two protein side chains as iron ligands despite accompanying structural perturbations. Access to various redox pairs and different responses to pH make this protein an excellent test case for energetic and dynamic studies of heme ligation.
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Affiliation(s)
- Dillon B Nye
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Eric A Johnson
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Melissa H Mai
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Juliette T J Lecomte
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
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