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Gupta A, Mardi P, Mishra PKK, Kumar A, Kumar R, Mahapatra A, Jena A, Behera PC. Evaluation of supplemented protein-L-isoaspartate-O-methyltransferase ( PIMT) gene of Carica papaya and Ricinus communis in stress survival of Escherichia coli BL21(DE3) cells. Prep Biochem Biotechnol 2024; 54:882-895. [PMID: 38170207 DOI: 10.1080/10826068.2023.2297692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In growing plant population, effect of stress is a perturb issue affecting its physiological, biochemical, yield loss and developmental growth. Protein-L-isoaspartate-O-methyltransferase (PIMT) is a broadly distributed protein repair enzyme which actuate under stressful environment or aging. Stress can mediate damage converting protein bound aspartate (Asp) residues to isoaspartate (iso-Asp). This spontaneous and deleterious conversion occurs at an elevated state of stress and aging. Iso-Asp formation is associated with protein inactivation and compromised cellular survival. PIMT can convert iso-Asp back to Asp, thus repairing and contributing to cellular survival. The present work describes the isolation, cloning, sequencing and expression of PIMT genes of Carica papaya (Cp pimt) and Ricinus communis (Rc pimt) Using gene specific primers, both the pimts were amplified from their respective cDNAs and subsequently cloned in prokaryotic expression vector pProEXHTa. BL21(DE3) strain of E. coli cells were used as expression host. The expression kinetics of both the PIMTs were studied with various concentrations of IPTG and at different time points. Finally, the PIMT supplemented BL21(DE3) cells were evaluated against different stresses in comparison to their counterparts with the empty vector control.
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Affiliation(s)
- Akanksha Gupta
- Plant Biotechnology, Department of Genetics and Plant Breeding, Banaras Hindu University, Mirzapur, India
| | - Pragati Mardi
- Plant Biotechnology, Department of Genetics and Plant Breeding, Banaras Hindu University, Mirzapur, India
| | - Prasanta Kumar Koustasa Mishra
- Unit of Teaching Veterinary Clinical Complex, Faculty of Veterinary and Animal Sciences, Banaras Hindu University, Mirzapur, India
| | - Anshuman Kumar
- Department of Animal Genetics and Breeding, Faculty of Veterinary and Animal Sciences, Banaras Hindu University, Mirzapur, India
| | - Rajesh Kumar
- Plant Biotechnology, Department of Genetics and Plant Breeding, Banaras Hindu University, Mirzapur, India
| | - Archana Mahapatra
- Department of Veterinary Anatomy, Faculty of Veterinary and Animal Sciences, Banaras Hindu University, Mirzapur, India
| | - Anupama Jena
- Fisheries and Animal Resource Development Department, Bhubaneswar, India
| | - Prakash Chandra Behera
- Department of Veterinary Biochemistry, College of Veterinary Science and Animal Husbandry, OUAT, Bhubaneshwar, India
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Chatterjee S, Bandyopadhyay A. Synthesis and characterization of two potential impurities (des-ethyl-Ganirelix) generated in the Ganirelix manufacturing process. J Pept Sci 2023; 29:e3489. [PMID: 36967632 DOI: 10.1002/psc.3489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Controlling certain diseases using peptide drugs has remarkably increased in the past two decades. In this regard, a generic formulation is an upfront solution to fulfill market demands. Ganirelix, a leading peptide active pharmaceutical ingredient (API) primarily used as a gonadotropin-releasing hormone antagonist (GnRH), has established a potential market value worldwide. But its generic formulation mandates detailed impurity profiles from a synthetic source and contemplates the sameness of a reference-listed drug (RLD). Post-chemical synthesis and processing of Ganirelix, some commercial sources have revealed two new potential impurities among many known, which show the deletion of an ethyl group from the hArg(Et)2 residue at the sixth and eighth positions, named des-ethyl-Ganirelix. These impurities are unprecedented in traditional peptide chemistry, and such monoethylated-hArg building blocks are not easily accessible commercially to synthesize these two impurities. Here, we have outlined the synthesis, purification, and enantiomeric purity characterization of the amino acids and their incorporation in the Ganirelix peptide sequence to synthesize these potential peptide impurities. This methodology will enable the convenient synthesis of side-chain substituted Arg and hArg derivatives in peptide drug discovery platforms.
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Affiliation(s)
- Saurav Chatterjee
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab, India
| | - Anupam Bandyopadhyay
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab, India
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Andino MS, Mora JR, Paz JL, Márquez EA, Perez-Castillo Y, Agüero-Chapin G. Elucidating the Racemization Mechanism of Aliphatic and Aromatic Amino Acids by In Silico Tools. Int J Mol Sci 2023; 24:11877. [PMID: 37569252 PMCID: PMC10418343 DOI: 10.3390/ijms241511877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
The racemization of biomolecules in the active site can reduce the biological activity of drugs, and the mechanism involved in this process is still not fully comprehended. The present study investigates the impact of aromaticity on racemization using advanced theoretical techniques based on density functional theory. Calculations were performed at the ωb97xd/6-311++g(d,p) level of theory. A compelling explanation for the observed aromatic stabilization via resonance is put forward, involving a carbanion intermediate. The analysis, employing Hammett's parameters, convincingly supports the presence of a negative charge within the transition state of aromatic compounds. Moreover, the combined utilization of natural bond orbital (NBO) analysis and intrinsic reaction coordinate (IRC) calculations confirms the pronounced stabilization of electron distribution within the carbanion intermediate. To enhance our understanding of the racemization process, a thorough examination of the evolution of NBO charges and Wiberg bond indices (WBIs) at all points along the IRC profile is performed. This approach offers valuable insights into the synchronicity parameters governing the racemization reactions.
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Affiliation(s)
- Mateo S. Andino
- Department of Chemical Engineering, Universidad San Francisco de Quito USFQ, Diego de Robles s/n y Av. Interoceánica, Quito 170157, Ecuador;
| | - José R. Mora
- Department of Chemical Engineering, Universidad San Francisco de Quito USFQ, Diego de Robles s/n y Av. Interoceánica, Quito 170157, Ecuador;
| | - José L. Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru;
| | - Edgar A. Márquez
- Grupo de Investigaciones en Química y Biología, Departamento de Química y Biología, Facultad de Ciencias Exactas, Universidad del Norte, Carrera 51B, Km 5, Vía Puerto Colombia, Barranquilla 081007, Colombia
| | - Yunierkis Perez-Castillo
- Bio-Chemoinformatics Research Group and Escuela de Ciencias Físicas y Matemáticas, Universidad de Las Américas, Quito 170504, Ecuador;
| | - Guillermin Agüero-Chapin
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Porto, Portugal;
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
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Morvan M, Mikšík I. The chiral proteomic analysis applied to aging collagens by LC-MS: Amino acid racemization, post-translational modifications, and sequence degradations during the aging process. Anal Chim Acta 2023; 1262:341260. [PMID: 37179063 DOI: 10.1016/j.aca.2023.341260] [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: 03/02/2023] [Revised: 04/14/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023]
Abstract
Collagen is the most abundant protein in the animal and human bodies, and it is not exempt from this aging phenomenon. Some age-related changes may appear on collagen sequences, such as increased surface hydrophobicity, the appearance of post-translational modifications, and amino acids racemization. This study has shown that the protein hydrolysis under deuterium conditions is privileged to limit the natural racemization during the hydrolysis. Indeed, under the deuterium condition, the homochirality of recent collagens is preserved whose amino acids are found in their L-form. However, in aging collagen, a natural amino acid racemization was observed. These results confirmed that the % d-amino acids are progressive according to age. The collagen sequence is degraded over time, and a fifth of the sequence information is lost during aging. Post-translational modifications (PTMs) in aging collagens can be a hypothesis to explain the modification of the hydrophobicity of the protein with the decrease of hydrophilic groups and the increase of hydrophobic groups. Finally, the exact positions of d-amino acids and PTMs have been correlated and elucidated.
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Affiliation(s)
- Marine Morvan
- Institute of Physiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic; Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10, Pardubice, Czech Republic.
| | - Ivan Mikšík
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10, Pardubice, Czech Republic
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Fundamental Cause of Bio-Chirality: Space-Time Symmetry—Concept Review. Symmetry (Basel) 2022. [DOI: 10.3390/sym15010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The search for fundamental determinants of bio-molecular chirality is a hot topic in biology, clarifying the meaning of evolution and the enigma of life’s origin. The question of origin may be resolved assuming that non-biological and biological entities obey nature’s universal laws grounded on space-time symmetry (STS) and space-time relativity (SPR). The fabric of STS is our review’s primary subject. This symmetry, encompassing the behavior of elementary particles and galaxy structure, imposes its fundamental laws on all hierarchical levels of the biological world. From the perspective of STS, objects across spatial scales may be classified as chiral or achiral concerning a specific space-related symmetry transformation: mirror reflection. The chiral object is not identical (i.e., not superimposable) to its mirror image. In geometry, distinguish two kinds of chiral objects. The first one does not have any reflective symmetry elements (a point or plane of symmetry) but may have rotational symmetry axes (dissymmetry). The second one does not have any symmetry elements (asymmetry). As the form symmetry deficiency, Chirality is the critical structural feature of natural systems, including sub-atomic particles and living matter. According to the Standard Model (SM) theory and String Theory (StrT), elementary particles associated with the four fundamental forces of nature determine the existence of micro- and galaxy scales of nature. Therefore, the inheritance of molecular symmetry from the symmetry of elementary particles indicates a bi-directional (internal [(micro-scale) and external (galaxy sale)] causal pathway of prevalent bio-chirality. We assume that the laws of the physical world impact the biological matter’s appearance through both extremities of spatial dimensions. The extended network of multi-disciplinary experimental evidence supports this hypothesis. However, many experimental results are derived and interpreted based on the narrow-view prerogative and highly specific terminology. The current review promotes a holistic approach to experimental results in two fast-developing, seemingly unrelated, divergent branches of STS and biological chirality. The generalized view on the origin of prevalent bio-molecular chirality is necessary for understanding the link between a diverse range of biological events. The chain of chirality transfer links ribosomal protein synthesis, cell morphology, and neuronal signaling with the laterality of cognitive functions.
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Dyakin VV, Uversky VN. Arrow of Time, Entropy, and Protein Folding: Holistic View on Biochirality. Int J Mol Sci 2022; 23:ijms23073687. [PMID: 35409047 PMCID: PMC8998916 DOI: 10.3390/ijms23073687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
Chirality is a universal phenomenon, embracing the space–time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are determined by utilizing the energy stored, transferred, and released, via adenosine triphosphate (ATP). At the protein level, the synthesis of a homochiral polypeptide chain of L-amino acids (L-AAs) represents the first state in the evolution of the dynamic non-equilibrium state of the system. At the next step the non-equilibrium state of a protein-centric system is supported and amended by a broad set of posttranslational modifications (PTMs). The enzymatic phosphorylation, being the most abundant and ATP-driven form of PTMs, illustrates the principal significance of the energy-coupling, in maintaining and reshaping the system. However, the physiological functions of phosphorylation are under the permanent risk of being compromised by spontaneous racemization. Therefore, the major distinct steps in protein-centric aging include the biosynthesis of a polypeptide chain, protein folding assisted by the system of PTMs, and age-dependent spontaneous protein racemization and degradation. To the best of our knowledge, we are the first to pay attention to the biphasic, alternative, and stepwise changes in the conformational entropy of protein folding. The broader view on protein folding, including the impact of spontaneous racemization, will help in the goal-oriented experimental design in the field of chiral proteomics.
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Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Bldg, 35, Orangeburg, NY 10962, USA
- Correspondence:
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA;
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Dyakin VV, Dyakina-Fagnano NV, Mcintire LB, Uversky VN. Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology. Int J Mol Sci 2021; 23:ijms23010285. [PMID: 35008708 PMCID: PMC8745688 DOI: 10.3390/ijms23010285] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/24/2021] [Accepted: 12/22/2021] [Indexed: 12/23/2022] Open
Abstract
In humans, age-associated degrading changes, widely observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psychological abilities, and memory. Cross-talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, genome, proteome, and lipidome instability are widely recognized as the primary causal factors in aging. We narrow attention to the roles of protein aging linked to prevalent amino acids chirality, enzymatic and spontaneous (non-enzymatic) post-translational modifications (PTMs SP), and non-equilibrium phase transitions. The homochirality of protein synthesis, resulting in the steady-state non-equilibrium condition of protein structure, makes them prone to multiple types of enzymatic and spontaneous PTMs, including racemization and isomerization. Spontaneous racemization leads to the loss of the balanced prevalent chirality. Advanced biological aging related to irreversible PTMs SP has been associated with the nontrivial interplay between somatic (molecular aging) and mental (psychological aging) health conditions. Through stress response systems (SRS), the environmental and psychological stressors contribute to the age-associated “collapse” of protein homochirality. The role of prevalent protein chirality and entropy of protein folding in biological aging is mainly overlooked. In a more generalized context, the time-dependent shift from enzymatic to the non-enzymatic transformation of biochirality might represent an important and yet underappreciated hallmark of aging. We provide the experimental arguments in support of the racemization theory of aging.
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Affiliation(s)
- Victor V. Dyakin
- The Nathan S. Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Bldg, 35, Bld. 35. Rom 201-C, Orangeburg, NY 10962, USA
- Correspondence: ; Tel.: +1-845-548-96-94; Fax: +1-845-398-5510
| | - Nuka V. Dyakina-Fagnano
- Child, Adolescent and Young Adult Psychiatry, 36 Franklin Turnpike, Waldwick, NJ 07463, USA;
| | - Laura B. Mcintire
- Department of Pathology and Cell Biology, Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA;
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA;
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