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Zhang J, Qiu W, Hu F, Zhang X, Deng Y, Nie H, Xu R. The rs2619566, rs10260404, and rs79609816 Polymorphisms Are Associated With Sporadic Amyotrophic Lateral Sclerosis in Individuals of Han Ancestry From Mainland China. Front Genet 2021; 12:679204. [PMID: 34421992 PMCID: PMC8378233 DOI: 10.3389/fgene.2021.679204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/25/2021] [Indexed: 11/21/2022] Open
Abstract
The pathogenesis of sporadic amyotrophic lateral sclerosis (sALS) remains unknown; however, recent research suggests that genetic factors may play an important role. This study aimed at investigating possible genetic risk factors for the pathogenesis of sALS. In our previous study, we conducted a genome-wide association study (GWAS) in 250 sALS patients and 250 control participants of Han ancestry from mainland China (HACM) and retrospectively analyzed the previously reported candidate loci related with sALS including our GWAS investigated results. In this study, twenty-seven candidate loci that were most likely associated with sALS were selected for further analysis in an independent case/control population of 239 sALS patients and 261 control subjects of HACM ethnicity using sequenom massARRAY methodology and DNA sequencing. We discovered that the polymorphism rs2619566 located within the contactin-4 (CNTN4) gene, rs10260404 in the dipeptidyl-peptidase 6 (DPP6) gene, and rs79609816 in the inositol polyphosphate-5-phosphatase B (INPP5B) gene were strongly associated with sALS in subjects of HACM ethnicity. Subjects harboring the minor C allele of rs2619566 and the minor T allele of rs79609816 exhibited an increased risk for sALS development, while carriers of the minor C allele of rs10260404 showed a decreased risk of sALS development compared to the subjects of other genotypes. The polymorphisms of rs2619566, rs10260404, and rs79609816 may change or affect the splicing, transcription, and translation of CNTN4, DPP6, and INPP5B genes and may play roles in the pathogenesis of sALS roles in the pathogenesis of sALS.
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Affiliation(s)
- Jie Zhang
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Weiwen Qiu
- Department of Neurology, The Affiliated People's Hospital of Nanchang University, The First Affiliated Hospital of Nanchang Medical College, Jiangxi Provincial People's Hospital, Nanchang, China
| | - Fan Hu
- Department of Neurology, The Affiliated People's Hospital of Nanchang University, The First Affiliated Hospital of Nanchang Medical College, Jiangxi Provincial People's Hospital, Nanchang, China
| | - Xiong Zhang
- Department of Neurology, Maoming People's Hospital, Maoming, China
| | - Youqing Deng
- Department of Neurology, The Third Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hongbing Nie
- Department of Neurology, The Affiliated People's Hospital of Nanchang University, The First Affiliated Hospital of Nanchang Medical College, Jiangxi Provincial People's Hospital, Nanchang, China
| | - Renshi Xu
- Department of Neurology, The Affiliated People's Hospital of Nanchang University, The First Affiliated Hospital of Nanchang Medical College, Jiangxi Provincial People's Hospital, Nanchang, China
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Mikulska-Ruminska K, Kulik AJ, Benadiba C, Bahar I, Dietler G, Nowak W. Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD. Sci Rep 2017; 7:8852. [PMID: 28821864 PMCID: PMC5562865 DOI: 10.1038/s41598-017-09482-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 07/27/2017] [Indexed: 01/06/2023] Open
Abstract
Contactin-4 (CNTN4) is a complex cell adhesion molecule (CAM) localized at neuronal membranes, playing a key role in maintaining the mechanical integrity and signaling properties of the synapse. CNTN4 consists of six immunoglobulin C2 type (IgC2) domains and four fibronectin type III (FnIII) domains that are shared with many other CAMs. Mutations in CNTN4 gene have been linked to various psychiatric disorders. Toward elucidating the response of this modular protein to mechanical stress, we studied its force-induced unfolding using single molecule atomic force microscopy (smAFM) and steered molecular dynamics (SMD) simulations. Extensive smAFM and SMD data both indicate the distinctive mechanical behavior of the two types of modules distinguished by unique force-extension signatures. The data also reveal the heterogeneity of the response of the individual FNIII and IgC2 modules, which presumably plays a role in the adaptability of CNTN4 to maintaining cell-cell communication and adhesion properties under different conditions. Results show that extensive sampling of force spectra, facilitated by robot-enhanced AFM, can help reveal the existence of weak stabilizing interactions between the domains of multidomain proteins, and provide insights into the nanomechanics of such multidomain or heteromeric proteins.
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Affiliation(s)
- Karolina Mikulska-Ruminska
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland. .,Institute of Physics, Faculty of Physics, Astronomy and Applied Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland. .,Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Biomedical Science Tower 3, Pittsburgh, PA, 15213, USA.
| | - Andrej J Kulik
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Carine Benadiba
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, Biomedical Science Tower 3, Pittsburgh, PA, 15213, USA.
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Applied Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
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Golas EI, Czaplewski C. Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk-based biopolymer. Biopolymers 2014; 101:915-23. [PMID: 24723330 DOI: 10.1002/bip.22494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/26/2014] [Accepted: 03/20/2014] [Indexed: 11/08/2022]
Abstract
This work theoretically investigates the mechanical properties of a novel silk-derived biopolymer as polymerized in silico from sericin and elastin-like monomers. Molecular Dynamics simulations and Steered Molecular Dynamics were the principal computational methods used, the latter of which applies an external force onto the system and thereby enables an observation of its response to stress. The models explored herein are single-molecule approximations, and primarily serve as tools in a rational design process for the preliminary assessment of properties in a new material candidate.
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Affiliation(s)
- Ewa I Golas
- Department of Chemistry, University of Gdańsk, Ul. Wita Stwosza 63, 80-308, Gdańsk, Poland
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Nanomechanics of β-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods. J Mol Model 2014; 20:2144. [PMID: 24562857 PMCID: PMC3964301 DOI: 10.1007/s00894-014-2144-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 01/12/2014] [Indexed: 11/25/2022]
Abstract
Computer simulations of protein unfolding substantially help to interpret force-extension curves measured in single-molecule atomic force microscope (AFM) experiments. Standard all-atom (AA) molecular dynamics simulations (MD) give a good qualitative mechanical unfolding picture but predict values too large for the maximum AFM forces with the common pulling speeds adopted here. Fine tuned coarse-grain MD computations (CG MD) offer quantitative agreement with experimental forces. In this paper we address an important methodological aspect of MD modeling, namely the impact of numerical noise generated by random assignments of bead velocities on maximum forces (Fmax) calculated within the CG MD approach. Distributions of CG forces from 2000 MD runs for several model proteins rich in β structures and having folds with increasing complexity are presented. It is shown that Fmax have nearly Gaussian distributions and that values of Fmax for each of those β-structures may vary from 93.2 ± 28.9 pN (neurexin) to 198.3 ± 25.2 pN (fibronectin). The CG unfolding spectra are compared with AA steered MD data and with results of our AFM experiments for modules present in contactin, fibronectin and neurexin. The stability of these proteins is critical for the proper functioning of neuronal synaptic clefts. Our results confirm that CG modeling of a single molecule unfolding is a good auxiliary tool in nanomechanics but large sets of data have to be collected before reliable comparisons of protein mechanical stabilities are made. Computational strechnings of single protein modeules leads to broad distributions of unfolding forces ![]()
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Molecular basis of lateral force spectroscopy nano-diagnostics: computational unbinding of autism related chemokine MCP-1 from IgG antibody. J Mol Model 2013; 19:4773-80. [PMID: 24061853 PMCID: PMC3825506 DOI: 10.1007/s00894-013-1972-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 08/01/2013] [Indexed: 12/05/2022]
Abstract
Monocyte-chemoattractant protein-1 (MCP-1), also known as CCL2, is a potent chemoattractant of T cells and monocytes, involved in inflammatory and angio-proliferative brain and retinal diseases. Higher expression of MCP-1 is observed in metastatic tumors. Unusual levels of MCP-1 in the brain may be correlated with autism. Immunochemistry where atomic force microscope (AFM) tips functionalized with appropriate antibodies against MCP-1 are used could in principle support medical diagnostics. Useful signals from single molecule experiments may be generated if interaction forces are large enough. The chemokine-antibody unbinding force depends on a relative motion of the interacting fragments of the complex. In this paper the stability of the medically important MCP-1- immunoglobulin G antibody Fab fragment complex has been studied using steered molecular dynamics (SMD) computer simulations with the aim to model possible arrangements of nano-diagnostics experiments. Using SMD we confirm that molecular recognition in MCP1-IgG is based mainly on six pairs of residues: Glu39A - Arg98H, Lys56A - Asp52H, Asp65A - Arg32L, Asp68A - Arg32L, Thr32A - Glu55L, Gln61A - Tyr33H. The minimum external force required for mechanical dissociation of the complex depends on a direction of the force. The pulling of the MCP-1 antigen in the directions parallel to the antigen-antibody contact plane requires forces about 20 %–40 % lower than in the perpendicular one. Fortunately, these values are large enough that the fast lateral force spectroscopy may be used for effective nano-diagnostics purposes. We show that molecular modeling is a useful tool in planning AFM force spectroscopy experiments. Lateral SMD forces (green arrow) required for mechanical unbinding of MCP-1 chemokine (blue) from Ig G antibody (red/gray) are 20-40% lower than vertical ones (orange arrow) ![]()
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Mercati O, Danckaert A, André-Leroux G, Bellinzoni M, Gouder L, Watanabe K, Shimoda Y, Grailhe R, De Chaumont F, Bourgeron T, Cloëz-Tayarani I. Contactin 4, -5 and -6 differentially regulate neuritogenesis while they display identical PTPRG binding sites. Biol Open 2013; 2:324-34. [PMID: 23519440 PMCID: PMC3603414 DOI: 10.1242/bio.20133343] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 11/28/2012] [Indexed: 12/22/2022] Open
Abstract
The neural cell-adhesion molecules contactin 4, contactin 5 and contactin 6 are involved in brain development, and disruptions in contactin genes may confer increased risk for autism spectrum disorders (ASD). We describe a co-culture of rat cortical neurons and HEK293 cells overexpressing and delivering the secreted forms of rat contactin 4-6. We quantified their effects on the length and branching of neurites. Contactin 4-6 effects were different depending on the contactin member and duration of co-culture. At 4 days in culture, contactin 4 and -6 increased the length of neurites, while contactin 5 increased the number of roots. Up to 8 days in culture, contactin 6 progressively increased the length of neurites while contactin 5 was more efficient on neurite branching. We studied the molecular sites of interaction between human contactin 4, -5 or -6 and the human Protein Tyrosine Phosphatase Receptor Gamma (PTPRG), a contactin partner, by modeling their 3D structures. As compared to contactin 4, we observed differences in the Ig2 and Ig3 domains of contactin 5 and -6 with the appearance of an omega loop that could adopt three distinct conformations. However, interactive residues between human contactin 4-6 and PTPRG were strictly conserved. We did not observe any differences in PTPRG binding on contactin 5 and -6 either. Our data suggest that the differential contactin effects on neurite outgrowth do not result from distinct interactions with PTPRG. A better understanding of the contactin cellular properties should help elucidate their roles in ASD.
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Affiliation(s)
- Oriane Mercati
- Human Genetics and Cognitive Functions, Institut Pasteur , 75015 Paris , France ; CNRS URA 2182 'Genes, synapses and cognition', Institut Pasteur , 75015 Paris , France ; Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions , 75013 Paris , France
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XU G, WU MH, LI GY. Progress of LRR Transmembrance Protein Function in Nervous System*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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