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Lei S, Zhang Y. Identification of the key genes and pathways involved in B cells in primary Sjögren' s syndrome. Bioengineered 2021; 12:2055-2073. [PMID: 34034637 PMCID: PMC8806908 DOI: 10.1080/21655979.2021.1930753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Primary Sjögren’ s syndrome (pSS) is a relatively common autoimmune disease, which mainly involves the exocrine glands, causing dry eye, dryness of mouth, fatigue and pain in the joints, thus severely affecting the normal lives of patients. B cell populations are considered to play an important role in their pathogenesis and pSS patients are generally characterized by exhibiting biological signs of B cell activation. Moreover, another important characterized change in the peripheral blood of pSS patients is found to be the decreased number of circulating memory B cells. However, the mechanisms underlying the B cell activation and the decreased level of circulating memory B cells in pSS patients are still unclear. Therefore, we identified key genes and pathways involved in B cells in pSS through a combination of several bioinformatic approaches including Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) and weighted gene co-expression network analysis (WGCNA) using gene expression data of pSS patients and controls from an open database Gene Expression Omnibus (GEO). The results may provide some novel insights into the pathogenesis of pSS. Moreover, we constructed and validated a diagnostic model for pSS by using the expression patterns of these key genes, which may assist clinicians in diagnosing pSS.
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Affiliation(s)
- Shizhen Lei
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Yi Zhang
- Department of Gerontology and Geriatrics, Shengjing Hospital of China Medical University, Shenyang, China
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Matsushima N, Miyashita H, Kretsinger RH. Sequence features, structure, ligand interaction, and diseases in small leucine rich repeat proteoglycans. J Cell Commun Signal 2021; 15:519-531. [PMID: 33860400 DOI: 10.1007/s12079-021-00616-4] [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] [Received: 02/13/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022] Open
Abstract
Small leucine rich repeat proteoglycans (SLRPs) are a group of active components of the extracellular matrix in all tissues. SLRPs bind to collagens and regulate collagen fibril growth and fibril organization. SLRPs also interact with various cytokines and extracellular compounds, which lead to various biological functions such cell adhesion and signaling, proliferation, and differentiation. Mutations in SLRP genes are associated with human diseases. Now crystal structures of five SLRPs are available. We describe some features of amino acid sequence and structures of SLRPs. We also review ligand interactions and then discuss the interaction surfaces. Furthermore, we map mutations associated with human diseases and discuss possible effects on structures by the mutations.
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Affiliation(s)
- Norio Matsushima
- Division of Bioinformatics, Institute of Tandem Repeats, Noboribetsu, 059-0464, Japan.
- Center for Medical Education, Sapporo Medical University, Sapporo, 060-8556, Japan.
| | - Hiroki Miyashita
- Division of Bioinformatics, Institute of Tandem Repeats, Noboribetsu, 059-0464, Japan
- Hokubu Rinsho Co., Ltd, Sapporo, 060⎼0061, Japan
| | - Robert H Kretsinger
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
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Flower TG, Hurley JH. Crystallographic molecular replacement using an in silico-generated search model of SARS-CoV-2 ORF8. Protein Sci 2021; 30:728-734. [PMID: 33625752 PMCID: PMC7980513 DOI: 10.1002/pro.4050] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 12/01/2022]
Abstract
The majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre-existing experimentally determined structures are used as search models. In favorable cases, ab initio predicted structures have yielded search models adequate for MR. The ORF8 protein of SARS-CoV-2 represents a challenging case for MR using an ab initio prediction because ORF8 has an all β-sheet fold and few orthologs. We previously determined experimentally the structure of ORF8 using the single anomalous dispersion (SAD) phasing method, having been unable to find an MR solution to the crystallographic phase problem. Following a report of an accurate prediction of the ORF8 structure, we assessed whether the predicted model would have succeeded as an MR search model. A phase problem solution was found, and the resulting structure was refined, yielding structural parameters equivalent to the original experimental solution.
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Affiliation(s)
- Thomas G. Flower
- Department of Molecular and Cell Biology and California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - James H. Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCaliforniaUSA
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Flower TG, Hurley JH. Crystallographic molecular replacement using an in silico-generated search model of SARS-CoV-2 ORF8. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.05.425441. [PMID: 33442695 PMCID: PMC7805452 DOI: 10.1101/2021.01.05.425441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre-existing experimentally determined structures are used as search models. In favorable cases, ab initio predicted structures have yielded search models adequate for molecular replacement. The ORF8 protein of SARS-CoV-2 represents a challenging case for MR using an ab initio prediction because ORF8 has an all β-sheet fold and few orthologs. We previously determined experimentally the structure of ORF8 using the single anomalous dispersion (SAD) phasing method, having been unable to find an MR solution to the crystallographic phase problem. Following a report of an accurate prediction of the ORF8 structure, we assessed whether the predicted model would have succeeded as an MR search model. A phase problem solution was found, and the resulting structure was refined, yielding structural parameters equivalent to the original experimental solution.
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Affiliation(s)
- Thomas G. Flower
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - James H. Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
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Structural basis of the leukocyte integrin Mac-1 I-domain interactions with the platelet glycoprotein Ib. Blood Adv 2020; 3:1450-1459. [PMID: 31053572 DOI: 10.1182/bloodadvances.2018027011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/10/2019] [Indexed: 12/14/2022] Open
Abstract
Cell-surface receptor interactions between leukocyte integrin macrophage-1 antigen (Mac-1, also known as CR3, αMβ2, CD11b/CD18) and platelet glycoprotein Ibα (GPIbα) are critical to vascular inflammation. To define the key residues at the binding interface, we used nuclear magnetic resonance (NMR) to assign the spectra of the mouse Mac-1 I-domain and mapped the residues contacting the mouse GPIbα N-terminal domain (GPIbαN) to the locality of the integrin metal ion-dependant adhesion site (MIDAS) surface. We next determined the crystal structures of the mouse GPIbαN and Mac-1 I-domain to 2 Å and 2.5 Å resolution, respectively. The mouse Mac-1 I-domain crystal structure reveals an active conformation that is stabilized by a crystal contact from the α7-helix with a glutamate side chain completing the octahedral coordination sphere of the MIDAS Mg2+ ion. The amino acid sequence of the α7-helix and disposition of the glutamic acid matches the C-terminal capping region α-helix of GPIbα effectively acting as a ligand mimetic. Using these crystal structures in combination with NMR measurements and docking analysis, we developed a model whereby an acidic residue from the GPIbα leucine-rich repeat (LRR) capping α-helix coordinates directly to the Mac-1 MIDAS Mg2+ ion. The Mac-1:GPIbαN complex involves additional interactions consolidated by an elongated pocket flanking the GPIbαN LRR capping α-helix. The GPIbαN α-helix has an HxxxE motif, which is equivalent by homology to RxxxD from the human GPIbαN. Subsequent mutagenesis of residues at this interface, coupled with surface plasmon resonance studies, confirmed the importance of GPIbαN residues H218, E222, and the Mac-1 MIDAS residue T209 to formation of the complex.
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Batkhishig D, Bilguun K, Enkhbayar P, Miyashita H, Kretsinger RH, Matsushima N. Super Secondary Structure Consisting of a Polyproline II Helix and a β-Turn in Leucine Rich Repeats in Bacterial Type III Secretion System Effectors. Protein J 2019; 37:223-236. [PMID: 29651716 PMCID: PMC5976695 DOI: 10.1007/s10930-018-9767-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Leucine rich repeats (LRRs) are present in over 100,000 proteins from viruses to eukaryotes. The LRRs are 20–30 residues long and occur in tandem. LRRs form parallel stacks of short β-strands and then assume a super helical arrangement called a solenoid structure. Individual LRRs are separated into highly conserved segment (HCS) with the consensus of LxxLxLxxNxL and variable segment (VS). Eight classes have been recognized. Bacterial LRRs are short and characterized by two prolines in the VS; the consensus is xxLPxLPxx with Nine residues (N-subtype) and xxLPxxLPxx with Ten residues (T-subtype). Bacterial LRRs are contained in type III secretion system effectors such as YopM, IpaH3/9.8, SspH1/2, and SlrP from bacteria. Some LRRs in decorin, fribromodulin, TLR8/9, and FLRT2/3 from vertebrate also contain the motifs. In order to understand structural features of bacterial LRRs, we performed both secondary structures assignments using four programs—DSSP-PPII, PROSS, SEGNO, and XTLSSTR—and HELFIT analyses (calculating helix axis, pitch, radius, residues per turn, and handedness), based on the atomic coordinates of their crystal structures. The N-subtype VS adopts a left handed polyproline II helix (PPII) with four, five or six residues and a type I β-turn at the C-terminal side. Thus, the N-subtype is characterized by a super secondary structure consisting of a PPII and a β-turn. In contrast, the T-subtype VS prefers two separate PPIIs with two or three and two residues. The HELFIT analysis indicates that the type I β-turn is a right handed helix. The HELFIT analysis determines three unit vectors of the helix axes of PPII (P), β-turn (B), and LRR domain (A). Three structural parameters using these three helix axes are suggested to characterize the super secondary structure and the LRR domain.
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Affiliation(s)
- Dashdavaa Batkhishig
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia.,Department of Physics, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, 210648, Mongolia
| | - Khurelbaatar Bilguun
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia.,Institute of Physics and Technology, Mongolian Academy of Sciences, Enkhtaivan avenue 54B, Ulaanbaatar, 210651, Mongolia
| | - Purevjav Enkhbayar
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia.
| | - Hiroki Miyashita
- Hokubu Rinsho Co., Ltd, Sapporo, 060-0061, Japan.,Institute of Tandem Repeats, Sapporo, 004-0882, Japan
| | | | - Norio Matsushima
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar, 14201, Mongolia. .,Institute of Tandem Repeats, Sapporo, 004-0882, Japan. .,Sapporo Medical University, Sapporo, 060-8556, Japan.
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Kaplan N, Yilmaz I, Karaarslan N, Kaya YE, Sirin DY, Ozbek H. Does Nimodipine, a Selective Calcium Channel Blocker, Impair Chondrocyte Proliferation or Damage Extracellular Matrix Structures? Curr Pharm Biotechnol 2019; 20:517-524. [PMID: 31057106 PMCID: PMC6751346 DOI: 10.2174/1389201020666190506124548] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/01/2019] [Accepted: 04/17/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND The study aimed to investigate the effects of the active ingredient, nimodipine, on chondrocyte proliferation and extracellular matrix (ECM) structures in cartilage tissue cells. METHODS Chondrocyte cultures were prepared from tissues resected via surgical operations. Nimodipine was then applied to these cultures and molecular analysis was performed. The data obtained were statistically calculated. RESULTS Both, the results of the (3-(4,5 dimethylthiazol2-yl)-2,5-diphenyltetrazolium (MTT) assay and the fluorescence microscope analysis [a membrane permeability test carried out with acridine orange/ propidium iodide staining (AO/PI)] confirmed that the active ingredient, nimodipine, negatively affects the cell cultures. CONCLUSION Nimodipine was reported to suppress cellular proliferation; chondroadherin (CHAD) and hypoxia-inducible factor-1 alpha (HIF-1α) expression thus decreased by 2.4 and 1.7 times, respectively, at 24 hrs when compared to the control group (p < 0.05). Furthermore, type II collagen (COL2A1) expression was not detected (p < 0.05). The risk that a drug prescribed by a clinician in an innocuous manner to treat a patient by relieving the symptoms of a disease may affect the proliferation, differentiation, and viability of other cells and/or tissues at the molecular level, beyond its known side effects or adverse events, should not be forgotten.
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Affiliation(s)
| | | | - Numan Karaarslan
- Address correspondence to this author at the Department of Neurosurgery, Namik Kemal University School of Medicine, 1-14 Campus Street, Tekirdag 59100, Turkey; Tel: +905057677266; Fax: +902822509950; E-mail:
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Milenković D, Avdović EH, Dimić D, Bajin Z, Ristić B, Vuković N, Trifunović SR, Marković ZS. Reactivity of the coumarine derivative towards cartilage proteins: combined NBO, QTAIM, and molecular docking study. MONATSHEFTE FUR CHEMIE 2017. [DOI: 10.1007/s00706-017-2051-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Paracuellos P, Kalamajski S, Bonna A, Bihan D, Farndale RW, Hohenester E. Structural and functional analysis of two small leucine-rich repeat proteoglycans, fibromodulin and chondroadherin. Matrix Biol 2017; 63:106-116. [PMID: 28215822 PMCID: PMC5618690 DOI: 10.1016/j.matbio.2017.02.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/09/2017] [Accepted: 02/09/2017] [Indexed: 02/07/2023]
Abstract
The small leucine-rich proteoglycans (SLRPs) are important regulators of extracellular matrix assembly and cell signalling. We have determined crystal structures at ~ 2.2 Å resolution of human fibromodulin and chondroadherin, two collagen-binding SLRPs. Their overall fold is similar to that of the prototypical SLRP, decorin, but unlike decorin neither fibromodulin nor chondroadherin forms a stable dimer. A previously identified binding site for integrin α2β1 maps to an α-helix in the C-terminal cap region of chondroadherin. Interrogation of the Collagen Toolkits revealed a unique binding site for chondroadherin in collagen II, and no binding to collagen III. A triple-helical peptide containing the sequence GAOGPSGFQGLOGPOGPO (O is hydroxyproline) forms a stable complex with chondroadherin in solution. In fibrillar collagen I and II, this sequence is aligned with the collagen cross-linking site KGHR, suggesting a role for chondroadherin in cross-linking. The crystal structures of fibromodulin and chondroadherin have been determined. Fibromodulin and chondroadherin are monomeric in solution. Chondroadherin binds to a unique site in type II collagen that contains the sequence GAOGPSGFQGLOGPOGPO (O, hydroxyproline). In collagen fibres, the chondroadherin binding site is adjacent to the cross-linking site, KGHR.
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Affiliation(s)
| | | | - Arkadiusz Bonna
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Dominique Bihan
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Richard W Farndale
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Erhard Hohenester
- Department of Life Sciences, Imperial College London, London, United Kingdom.
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