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Harrison SA, Naretto A, Balakrishnan S, Perera YR, Chazin WJ. Comparative analysis of the physical properties of murine and human S100A7: Insight into why zinc piracy is mediated by human but not murine S100A7. J Biol Chem 2023; 299:105292. [PMID: 37769710 PMCID: PMC10598741 DOI: 10.1016/j.jbc.2023.105292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023] Open
Abstract
S100 proteins are a subfamily of EF-hand calcium-binding proteins found primarily in vertebrate animals. They are distinguished by binding of transition metals and functioning in both the intracellular and extracellular milieu. S100A7 functions in the protection of the skin and mucous membranes and is a biomarker in inflammatory skin disease. A recent study of Neisseria gonorrhoeae infection revealed that human but not murine S100A7 could be used to evade host nutritional immunity. To understand the molecular basis for this difference, we carried out a comparative analysis of the physical and structural properties of human and murine S100A7. The X-ray crystal structure of Ca2+-loaded mouse S100A7 (mS100A7) was determined to 1.69 Å resolution, and Ca2+-induced conformational changes were assessed by NMR. Unlike human S100A7 (hS100A7), which exhibits conformational changes in response to binding of Ca2+, no significant changes in mS100A7 were detected. Dynamic light scattering, circular dichroism, and a competition chelator assay were used to compare the Zn2+ affinity and the effects of ion binding on mS100A7 versus hS100A7. Alignment of their sequences revealed a substantial difference in the C-terminal region, which is an important mediator of protein-protein interactions, suggesting a rationale for the specificity of N. gonorrhoeae for hS100A7. These data, along with more detailed analysis of S100A7 sequence conservation across different species, support the proposal that, although hS100A7 is highly conserved in many mammals, the murine protein is a distinct ortholog. Our results highlight the potential limitations of using mouse models for studying bacterial infections in humans.
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Affiliation(s)
- Simone A Harrison
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Anais Naretto
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Swati Balakrishnan
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Yasiru R Perera
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.
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Julian TH, Cooper-Knock J, MacGregor S, Guo H, Aslam T, Sanderson E, Black GCM, Sergouniotis PI. Phenome-wide Mendelian randomisation analysis identifies causal factors for age-related macular degeneration. eLife 2023; 12:82546. [PMID: 36705323 PMCID: PMC9883012 DOI: 10.7554/elife.82546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/18/2022] [Indexed: 01/28/2023] Open
Abstract
Background Age-related macular degeneration (AMD) is a leading cause of blindness in the industrialised world and is projected to affect >280 million people worldwide by 2040. Aiming to identify causal factors and potential therapeutic targets for this common condition, we designed and undertook a phenome-wide Mendelian randomisation (MR) study. Methods We evaluated the effect of 4591 exposure traits on early AMD using univariable MR. Statistically significant results were explored further using: validation in an advanced AMD cohort; MR Bayesian model averaging (MR-BMA); and multivariable MR. Results Overall, 44 traits were found to be putatively causal for early AMD in univariable analysis. Serum proteins that were found to have significant relationships with AMD included S100-A5 (odds ratio [OR] = 1.07, p-value = 6.80E-06), cathepsin F (OR = 1.10, p-value = 7.16E-05), and serine palmitoyltransferase 2 (OR = 0.86, p-value = 1.00E-03). Univariable MR analysis also supported roles for complement and immune cell traits. Although numerous lipid traits were found to be significantly related to AMD, MR-BMA suggested a driving causal role for serum sphingomyelin (marginal inclusion probability [MIP] = 0.76; model-averaged causal estimate [MACE] = 0.29). Conclusions The results of this MR study support several putative causal factors for AMD and highlight avenues for future translational research. Funding This project was funded by the Wellcome Trust (224643/Z/21/Z; 200990/Z/16/Z); the University of Manchester's Wellcome Institutional Strategic Support Fund (Wellcome ISSF) grant (204796/Z/16/Z); the UK National Institute for Health Research (NIHR) Academic Clinical Fellow and Clinical Lecturer Programmes; Retina UK and Fight for Sight (GR586); the Australian National Health and Medical Research Council (NHMRC) (1150144).
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Affiliation(s)
- Thomas H Julian
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
- Manchester Royal Eye Hospital, Manchester University NHS Foundation TrustManchesterUnited Kingdom
| | - Johnathan Cooper-Knock
- Department of Neuroscience, Sheffield Institute for Translational Neuroscience (SITraN), University of SheffieldSheffieldUnited Kingdom
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Hui Guo
- Centre for Biostatistics, Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Tariq Aslam
- Manchester Royal Eye Hospital, Manchester University NHS Foundation TrustManchesterUnited Kingdom
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, School of Health Sciences, University of ManchesterManchesterUnited Kingdom
| | - Eleanor Sanderson
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
| | - Graeme CM Black
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
- Manchester Centre for Genomic Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation TrustManchesterUnited Kingdom
| | - Panagiotis I Sergouniotis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
- Manchester Royal Eye Hospital, Manchester University NHS Foundation TrustManchesterUnited Kingdom
- Manchester Centre for Genomic Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation TrustManchesterUnited Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome CampusCambridgeUnited Kingdom
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Harman JL, Reardon PN, Costello SM, Warren GD, Phillips SR, Connor PJ, Marqusee S, Harms MJ. Evolution avoids a pathological stabilizing interaction in the immune protein S100A9. Proc Natl Acad Sci U S A 2022; 119:e2208029119. [PMID: 36194634 PMCID: PMC9565474 DOI: 10.1073/pnas.2208029119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/07/2022] [Indexed: 01/03/2023] Open
Abstract
Stability constrains evolution. While much is known about constraints on destabilizing mutations, less is known about the constraints on stabilizing mutations. We recently identified a mutation in the innate immune protein S100A9 that provides insight into such constraints. When introduced into human S100A9, M63F simultaneously increases the stability of the protein and disrupts its natural ability to activate Toll-like receptor 4. Using chemical denaturation, we found that M63F stabilizes a calcium-bound conformation of hS100A9. We then used NMR to solve the structure of the mutant protein, revealing that the mutation distorts the hydrophobic binding surface of hS100A9, explaining its deleterious effect on function. Hydrogen-deuterium exchange (HDX) experiments revealed stabilization of the region around M63F in the structure, notably Phe37. In the structure of the M63F mutant, the Phe37 and Phe63 sidechains are in contact, plausibly forming an edge-face π-stack. Mutating Phe37 to Leu abolished the stabilizing effect of M63F as probed by both chemical denaturation and HDX. It also restored the biological activity of S100A9 disrupted by M63F. These findings reveal that Phe63 creates a molecular staple with Phe37 that stabilizes a nonfunctional conformation of the protein, thus disrupting function. Using a bioinformatic analysis, we found that S100A9 proteins from different organisms rarely have Phe at both positions 37 and 63, suggesting that avoiding a pathological stabilizing interaction indeed constrains S100A9 evolution. This work highlights an important evolutionary constraint on stabilizing mutations, namely, that they must avoid inappropriately stabilizing nonfunctional protein conformations.
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Affiliation(s)
- Joseph L Harman
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Patrick N Reardon
- College of Science, NMR Facility, Oregon State University, Corvallis, OR 97331
| | - Shawn M Costello
- Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA 94720
| | - Gus D Warren
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Sophia R Phillips
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Patrick J Connor
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720
| | - Michael J Harms
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403
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Xu HY, Song HM, Zhou Q. Comprehensive analysis of the expression and prognosis for S100 in human ovarian cancer: A STROBE study. Medicine (Baltimore) 2020; 99:e22777. [PMID: 33217795 PMCID: PMC7676574 DOI: 10.1097/md.0000000000022777] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
S100 family members are frequently deregulated in human malignancies, including ovarian cancer. However, the prognostic roles of each individual S100 family member in ovarian cancer (OC) patients remain elusive. In the present study, we assessed the prognostic roles and molecular function of 20 individual members of the S100 family in OC patients using GEPIA, Kaplan-Meier plotter, SurvExpress, GeneMANIA and Funrich database. Our results indicated that the mRNA expression levels of S100A1, S100A2, S100A4, S100A5, S100A11, S100A14, and S100A16 were significantly upregulated in patients with OC, and high mRNA expression of S100A1, S100A3, S100A5, S100A6, and S100A13 were significantly correlated with better overall survival, while increased S100A2, S100A7A, S100A10, and S100A11 mRNA expressions were associated with worse prognosis in OC patients. In stratified analysis, the trends of high expression of individual S100 members were nearly the same in different pathological grade, clinical stage, TP53 mutation status, and treatment. More importantly, S100 family signatures may be useful potential prognostic markers for OC. These findings suggest that S100 family plays a vital role in prognostic value and could potentially be an S100-targeted inhibitors for OC patients.
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Affiliation(s)
- Hong-Yu Xu
- Department of Gynecology and Obstetrics, the Second People's Hospital of Yichang, China Three Gorges University
| | - Hua-Mei Song
- Department of Gynecology and Obstetrics, the People's Hospital of China Three Gorges University/the First People's Hospital of Yichang, Yichang, Hubei, China
| | - Quan Zhou
- Department of Gynecology and Obstetrics, the People's Hospital of China Three Gorges University/the First People's Hospital of Yichang, Yichang, Hubei, China
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Ite K, Yonezawa K, Kitanishi K, Shimizu N, Unno M. Optimal Mutant Model of Human S100A3 Protein Citrullinated at Arg51 by Peptidylarginine Deiminase Type III and Its Solution Structural Properties. ACS OMEGA 2020; 5:4032-4042. [PMID: 32149230 PMCID: PMC7057681 DOI: 10.1021/acsomega.9b03618] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/29/2020] [Indexed: 05/30/2023]
Abstract
S100A3 protein, a member of the EF-hand-type Ca2+-binding S100 protein family, undergoes a Ca2+-/Zn2+-induced structural change to a tetrameric state upon specific citrullination of R51 in human hair cuticular cells. To elucidate the underlying mechanism, we prepared recombinant mutant S100A3 proteins, including R51A, R51C, R51E, R51K, and R51Q, as potential models of post-translationally modified S100A3 and evaluated their biophysical and biochemical properties relative to wild-type (WT) S100A3 and WT citrullinated in vitro. Size exclusion chromatography (SEC) showed that R51Q formed a tetramer in the presence of Ca2+, while Ca2+ titration monitored by Trp fluorescence indicated that R51Q had Ca2+-binding properties similar to those of citrullinated S1003A. We therefore concluded that R51Q is the optimal mutant model of post-translationally modified S100A3. We compared the solution structure of WT S100A3 and the R51Q mutant in the absence and presence of Ca2+ and Zn2+ by SEC-small-angle X-ray scattering. The radius of gyration of R51Q in the metal-free state was almost the same as that of WT; however, it increased by ∼1.5-fold in the presence of Ca2+/Zn2+, indicating a large expansion in molecular size. By contrast, addition of Ca2+/Zn2+ to WT led to nonspecific aggregation in SEC analysis and dynamic light scattering, suggesting that citrullination of S100A3 is essential for stabilization of the Ca2+-/Zn2+-bound state. These findings will lead to the further development of structural analyses for the Ca2+-/Zn2+-bound S100A3.
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Affiliation(s)
- Kenji Ite
- Graduate
School of Science and Engineering, Ibaraki
University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
- Frontier
Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Naka, Ibaraki 319-1106, Japan
| | - Kento Yonezawa
- High
Energy Accelerator Research Organization, Institute of Materials Structure
Science, 1-1 Ohho, Tsukuba, Ibaraki 300-3256, Japan
| | - Kenichi Kitanishi
- Graduate
School of Science and Engineering, Ibaraki
University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
- Frontier
Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Naka, Ibaraki 319-1106, Japan
| | - Nobutaka Shimizu
- High
Energy Accelerator Research Organization, Institute of Materials Structure
Science, 1-1 Ohho, Tsukuba, Ibaraki 300-3256, Japan
| | - Masaki Unno
- Graduate
School of Science and Engineering, Ibaraki
University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
- Frontier
Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Naka, Ibaraki 319-1106, Japan
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Duvvuri H, Wheeler LC, Harms MJ. pytc: Open-Source Python Software for Global Analyses of Isothermal Titration Calorimetry Data. Biochemistry 2018; 57:2578-2583. [PMID: 29620867 PMCID: PMC5995568 DOI: 10.1021/acs.biochem.7b01264] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Here we describe pytc, an open-source Python package for global fits of thermodynamic models to multiple isothermal titration calorimetry experiments. Key features include simplicity, the ability to implement new thermodynamic models, a robust maximum likelihood fitter, a fast Bayesian Markov-Chain Monte Carlo sampler, rigorous implementation, extensive documentation, and full cross-platform compatibility. pytc fitting can be done using an application program interface or via a graphical user interface. It is available for download at https://github.com/harmslab/pytc .
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Affiliation(s)
- Hiranmayi Duvvuri
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Lucas C. Wheeler
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Michael J. Harms
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
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