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Seal S, Banerjee N, Mahato R, Kundu T, Sinha D, Chakraborty T, Sinha D, Sau K, Chatterjee S, Sau S. Serine 106 preserves the tertiary structure, function, and stability of a cyclophilin from Staphylococcus aureus. J Biomol Struct Dyn 2023; 41:1479-1494. [PMID: 34967275 DOI: 10.1080/07391102.2021.2021992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
SaCyp, a staphylococcal cyclophilin involved in both protein folding and pathogenesis, has a Ser residue at position 106 and a Trp residue at position 136. While Ser 106 of SaCyp aligned with a cyclosporin A (CsA) binding Ala residue, its Trp 136 aligned with a Trp or a Phe residue of most other cyclophilins. To demonstrate the exact roles of Ser 106 and Trp 136 in SaCyp, we have elaborately studied rCyp[S106A] and rCyp[W136A], two-point mutants of a recombinant SaCyp (rCyp) harboring an Ala substitution at positions 106 and 136, respectively. Of the mutants, rCyp[W136A] showed the rCyp-like CsA binding affinity and peptidyl-prolyl cis-trans isomerase (PPIase) activity. Conversely, the PPIase activity, CsA binding affinity, stability, tertiary structure, surface hydrophobicity, and Trp accessibility of rCyp[S106A] notably differed from those of rCyp. The computational experiments also reveal that the structure, dimension, and fluctuation of SaCyp are not identical to those of SaCyp[S106A]. Furthermore, Ser at position 106 of SaCyp, compared to Ala at the same position, formed a higher number of non-covalent bonds with CsA. Collectively, Ser 106 is an indispensable residue for SaCyp that keeps its tertiary structure, function, and stability intact.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soham Seal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biophysics, Bose Institute, Kolkata, West Bengal, India
| | - Rohit Mahato
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Tanmoy Kundu
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Debabrata Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | | | - Debasmita Sinha
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | | | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
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Pehrsson M, Mortensen JH, Manon-Jensen T, Bay-Jensen AC, Karsdal MA, Davies MJ. Enzymatic cross-linking of collagens in organ fibrosis - resolution and assessment. Expert Rev Mol Diagn 2021; 21:1049-1064. [PMID: 34330194 DOI: 10.1080/14737159.2021.1962711] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Enzymatic cross-linking of the collagens within the extracellular matrix (ECM) catalyzed by enzymes such as lysyl oxidase (LOX) and lysyl oxidase like-enzymes 1-4 (LOXL), transglutaminase 2 (TG2), and peroxidasin (PXDN) contribute to fibrosis progression through extensive collagen cross-linking. Studies in recent years have begun elucidating the important role of collagen cross-linking in perpetuating progression of organ fibrosis independently of inflammation through an increasingly stiff and noncompliant ECM. Therefore, collagen cross-linking and the cross-linking enzymes have become new targets in anti-fibrotic therapy as well as targets of novel biomarkers to properly assess resolution of the fibrotic ECM.Areas covered: The enzymatic actions of enzymes catalyzing collagen cross-linking and their relevance in organ fibrosis. Potential biomarkers specifically quantifying proteolytic fragments of collagen cross-linking is discussed based on Pubmed search done in November 2020 as well as the authors knowledge.Expert opinion: Current methods for the assessment of fibrosis involve the use of invasive and/or cumbersome and expensive methods such as tissue biopsies. Thus, an unmet need exists for the development and validation of minimally invasive biomarkers of proteolytic fragments of cross-linked collagens. These biomarkers may aid in the development and proper assessment of fibrosis resolution in coming years.
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Affiliation(s)
- Martin Pehrsson
- Department of Biomedical Science, University of Copenhagen, Copenhagen, Denmark.,Biomarkers & Research, Nordic Bioscience A/S, Herlev, Denmark
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Seal S, Chowdhury N, Biswas R, Chakraborty T, Sinha D, Bagchi A, Sau S. Removal of an atypical region from a staphylococcal cyclophilin affects its structure, function, stability, and shape. Int J Biol Macromol 2020; 151:1287-1298. [DOI: 10.1016/j.ijbiomac.2019.10.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/15/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
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Brinkman EL, Weed BC, Patnaik SS, Brazile BL, Centini RM, Wills RW, Olivier B, Sledge DG, Cooley J, Liao J, Rashmir-Raven AM. Cardiac findings in Quarter Horses with heritable equine regional dermal asthenia. J Am Vet Med Assoc 2017; 250:538-547. [DOI: 10.2460/javma.250.5.538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Gjaltema RAF, Bank RA. Molecular insights into prolyl and lysyl hydroxylation of fibrillar collagens in health and disease. Crit Rev Biochem Mol Biol 2016; 52:74-95. [PMID: 28006962 DOI: 10.1080/10409238.2016.1269716] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Collagen is a macromolecule that has versatile roles in physiology, ranging from structural support to mediating cell signaling. Formation of mature collagen fibrils out of procollagen α-chains requires a variety of enzymes and chaperones in a complex process spanning both intracellular and extracellular post-translational modifications. These processes include modifications of amino acids, folding of procollagen α-chains into a triple-helical configuration and subsequent stabilization, facilitation of transportation out of the cell, cleavage of propeptides, aggregation, cross-link formation, and finally the formation of mature fibrils. Disruption of any of the proteins involved in these biosynthesis steps potentially result in a variety of connective tissue diseases because of a destabilized extracellular matrix. In this review, we give a revised overview of the enzymes and chaperones currently known to be relevant to the conversion of lysine and proline into hydroxyproline and hydroxylysine, respectively, and the O-glycosylation of hydroxylysine and give insights into the consequences when these steps are disrupted.
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Affiliation(s)
- Rutger A F Gjaltema
- a MATRIX Research Group, Department of Pathology and Medical Biology , University Medical Center Groningen, University of Groningen , Groningen , the Netherlands
| | - Ruud A Bank
- a MATRIX Research Group, Department of Pathology and Medical Biology , University Medical Center Groningen, University of Groningen , Groningen , the Netherlands
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Rashmir-Raven AM, Spier SJ. Hereditary equine regional dermal asthenia (HERDA) in Quarter Horses: A review of clinical signs, genetics and research. EQUINE VET EDUC 2015. [DOI: 10.1111/eve.12459] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- A. M. Rashmir-Raven
- Large Animal Clinical Sciences; College of Veterinary Medicine; Michigan State University; East Lansing USA
| | - S. J. Spier
- Department of Medicine and Epidemiology; School of Veterinary Medicine; University of California; Davis USA
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Plant immunophilins: a review of their structure-function relationship. Biochim Biophys Acta Gen Subj 2014; 1850:2145-58. [PMID: 25529299 DOI: 10.1016/j.bbagen.2014.12.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/13/2014] [Accepted: 12/15/2014] [Indexed: 01/02/2023]
Abstract
BACKGROUND Originally discovered as receptors for immunosuppressive drugs, immunophilins consist of two major groups, FK506 binding proteins (FKBPs) and cyclosporin A binding proteins (cyclophilins, CYPs). Many members in both FKBP and CYP families are peptidyl prolyl isomerases that are involved in protein folding processes, though they share little sequence homology. It is not surprising to find immunophilins in all organisms examined so far, including viruses, bacteria, fungi, plants and animals, as protein folding represents a common process in all living systems. SCOPE OF REVIEW Studies on plant immunophilins have revealed new functions beyond protein folding and new structural properties beyond that of typical PPIases. This review focuses on the structural and functional diversity of plant FKBPs and CYPs. MAJOR CONCLUSIONS The differences in sequence, structure as well as subcellular localization, have added on to the diversity of this family of molecular chaperones. In particular, the large number of immunophilins present in the thylakoid lumen of the photosynthetic organelle, promises to deliver insights into the regulation of photosynthesis, a unique feature of plant systems. However, very little structural information and functional data are available for plant immunophilins. GENERAL SIGNIFICANCE Studies on the structure and function of plant immunophilins are important in understanding their role in plant biology. By reviewing the structural and functional properties of some immunophilins that represent the emerging area of research in plant biology, we hope to increase the interest of researchers in pursuing further research in this area. This article is part of a Special Issue entitled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets.
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Ishikawa Y, Bächinger HP. A substrate preference for the rough endoplasmic reticulum resident protein FKBP22 during collagen biosynthesis. J Biol Chem 2014; 289:18189-201. [PMID: 24821723 DOI: 10.1074/jbc.m114.561944] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The biosynthesis of collagens occurs in the rough endoplasmic reticulum and requires a large numbers of molecular chaperones, foldases, and post-translational modification enzymes. Collagens contain a large number of proline residues that are post-translationally modified to 3-hydroxyproline or 4-hydroxyproline, and the rate-limiting step in formation of the triple helix is the cis-trans isomerization of peptidyl-proline bonds. This step is catalyzed by peptidyl-prolyl cis-trans isomerases. There are seven peptidyl-prolyl cis-trans isomerases in the rER, and so far, two of these enzymes, cyclophilin B and FKBP65, have been shown to be involved in collagen biosynthesis. The absence of either cyclophilin B or FKBP65 leads to a recessive form of osteogenesis imperfecta. The absence of FKBP22 leads to a kyphoscoliotic type of Ehlers-Danlos syndrome (EDS), and this type of EDS is classified as EDS type VI, which can also be caused by a deficiency in lysyl-hydroxylase 1. However, the lack of FKBP22 shows a wider spectrum of clinical phenotypes than the absence of lysyl-hydroxylase 1 and additionally includes myopathy, hearing loss, and aortic rupture. Here we show that FKBP22 catalyzes the folding of type III collagen and interacts with type III collagen, type VI collagen, and type X collagen, but not with type I collagen, type II collagen, or type V collagen. These restrictive interactions might help explain the broader phenotype observed in patients that lack FKBP22.
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Affiliation(s)
- Yoshihiro Ishikawa
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and the Research Department, Shriners Hospital for Children, Portland, Oregon 97239
| | - Hans Peter Bächinger
- From the Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon 97239 and the Research Department, Shriners Hospital for Children, Portland, Oregon 97239
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