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Xia C, Braunstein Z, Toomey AC, Zhong J, Rao X. S100 Proteins As an Important Regulator of Macrophage Inflammation. Front Immunol 2018; 8:1908. [PMID: 29379499 PMCID: PMC5770888 DOI: 10.3389/fimmu.2017.01908] [Citation(s) in RCA: 243] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/14/2017] [Indexed: 12/17/2022] Open
Abstract
The S100 proteins, a family of calcium-binding cytosolic proteins, have a broad range of intracellular and extracellular functions through regulating calcium balance, cell apoptosis, migration, proliferation, differentiation, energy metabolism, and inflammation. The intracellular functions of S100 proteins involve interaction with intracellular receptors, membrane protein recruitment/transportation, transcriptional regulation and integrating with enzymes or nucleic acids, and DNA repair. The S100 proteins could also be released from the cytoplasm, induced by tissue/cell damage and cellular stress. The extracellular S100 proteins, serving as a danger signal, are crucial in regulating immune homeostasis, post-traumatic injury, and inflammation. Extracellular S100 proteins are also considered biomarkers for some specific diseases. In this review, we will discuss the multi-functional roles of S100 proteins, especially their potential roles associated with cell migration, differentiation, tissue repair, and inflammation.
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Affiliation(s)
- Chang Xia
- College of Health Science and Nursing, Wuhan Polytechnic University, Wuhan, China.,Cardiovascular Research Institute, Case Western Reserve University, Cleveland, OH, United States
| | - Zachary Braunstein
- Boonshoft School of Medicine, Wright State University, Dayton, OH, United States
| | - Amelia C Toomey
- Department of Health Sciences, University of Missouri, Columbia, MO, United States
| | - Jixin Zhong
- Cardiovascular Research Institute, Case Western Reserve University, Cleveland, OH, United States
| | - Xiaoquan Rao
- Cardiovascular Research Institute, Case Western Reserve University, Cleveland, OH, United States
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2
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Xia C, Braunstein Z, Toomey AC, Zhong J, Rao X. S100 Proteins As an Important Regulator of Macrophage Inflammation. Front Immunol 2017. [PMID: 29379499 DOI: 10.3389/fimmu.2017.01908/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
The S100 proteins, a family of calcium-binding cytosolic proteins, have a broad range of intracellular and extracellular functions through regulating calcium balance, cell apoptosis, migration, proliferation, differentiation, energy metabolism, and inflammation. The intracellular functions of S100 proteins involve interaction with intracellular receptors, membrane protein recruitment/transportation, transcriptional regulation and integrating with enzymes or nucleic acids, and DNA repair. The S100 proteins could also be released from the cytoplasm, induced by tissue/cell damage and cellular stress. The extracellular S100 proteins, serving as a danger signal, are crucial in regulating immune homeostasis, post-traumatic injury, and inflammation. Extracellular S100 proteins are also considered biomarkers for some specific diseases. In this review, we will discuss the multi-functional roles of S100 proteins, especially their potential roles associated with cell migration, differentiation, tissue repair, and inflammation.
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Affiliation(s)
- Chang Xia
- College of Health Science and Nursing, Wuhan Polytechnic University, Wuhan, China.,Cardiovascular Research Institute, Case Western Reserve University, Cleveland, OH, United States
| | - Zachary Braunstein
- Boonshoft School of Medicine, Wright State University, Dayton, OH, United States
| | - Amelia C Toomey
- Department of Health Sciences, University of Missouri, Columbia, MO, United States
| | - Jixin Zhong
- Cardiovascular Research Institute, Case Western Reserve University, Cleveland, OH, United States
| | - Xiaoquan Rao
- Cardiovascular Research Institute, Case Western Reserve University, Cleveland, OH, United States
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O'Reilly PG, Wen Q, Bankhead P, Dunne PD, McArt DG, McPherson S, Hamilton PW, Mills KI, Zhang SD. QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics. BMC Bioinformatics 2016; 17:198. [PMID: 27143038 PMCID: PMC4855472 DOI: 10.1186/s12859-016-1062-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022] Open
Abstract
Background Gene expression connectivity mapping has proven to be a powerful and flexible tool for research. Its application has been shown in a broad range of research topics, most commonly as a means of identifying potential small molecule compounds, which may be further investigated as candidates for repurposing to treat diseases. The public release of voluminous data from the Library of Integrated Cellular Signatures (LINCS) programme further enhanced the utilities and potentials of gene expression connectivity mapping in biomedicine. Results We describe QUADrATiC (http://go.qub.ac.uk/QUADrATiC), a user-friendly tool for the exploration of gene expression connectivity on the subset of the LINCS data set corresponding to FDA-approved small molecule compounds. It enables the identification of compounds for repurposing therapeutic potentials. The software is designed to cope with the increased volume of data over existing tools, by taking advantage of multicore computing architectures to provide a scalable solution, which may be installed and operated on a range of computers, from laptops to servers. This scalability is provided by the use of the modern concurrent programming paradigm provided by the Akka framework. The QUADrATiC Graphical User Interface (GUI) has been developed using advanced Javascript frameworks, providing novel visualization capabilities for further analysis of connections. There is also a web services interface, allowing integration with other programs or scripts. Conclusions QUADrATiC has been shown to provide an improvement over existing connectivity map software, in terms of scope (based on the LINCS data set), applicability (using FDA-approved compounds), usability and speed. It offers potential to biological researchers to analyze transcriptional data and generate potential therapeutics for focussed study in the lab. QUADrATiC represents a step change in the process of investigating gene expression connectivity and provides more biologically-relevant results than previous alternative solutions. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1062-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul G O'Reilly
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Qing Wen
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Peter Bankhead
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Darragh G McArt
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Suzanne McPherson
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Peter W Hamilton
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Ken I Mills
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK.
| | - Shu-Dong Zhang
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, BT9 7AE, UK. .,Northern Ireland Centre for Stratified Medicine, University of Ulster, C-TRIC Building, Altnagelvin Hospital campus, Glenshane Road, Derry/Londonderry, BT47 6SB, UK.
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Cau Y, Fiorillo A, Mori M, Ilari A, Botta M, Lalle M. Molecular Dynamics Simulations and Structural Analysis of Giardia duodenalis 14-3-3 Protein-Protein Interactions. J Chem Inf Model 2015; 55:2611-22. [PMID: 26551337 DOI: 10.1021/acs.jcim.5b00452] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Giardiasis is a gastrointestinal diarrheal illness caused by the protozoan parasite Giardia duodenalis, which affects annually over 200 million people worldwide. The limited antigiardial drug arsenal and the emergence of clinical cases refractory to standard treatments dictate the need for new chemotherapeutics. The 14-3-3 family of regulatory proteins, extensively involved in protein-protein interactions (PPIs) with pSer/pThr clients, represents a highly promising target. Despite homology with human counterparts, the single 14-3-3 of G. duodenalis (g14-3-3) is characterized by a constitutive phosphorylation in a region critical for target binding, thus affecting the function and the conformation of g14-3-3/clients interaction. However, to approach the design of specific small molecule modulators of g14-3-3 PPIs, structural elucidations are required. Here, we present a detailed computational and crystallographic study exploring the implications of g14-3-3 phosphorylation on protein structure and target binding. Self-Guided Langevin Dynamics and classical molecular dynamics simulations show that phosphorylation affects locally and globally g14-3-3 conformation, inducing a structural rearrangement more suitable for target binding. Profitable features for g14-3-3/clients interaction were highlighted using a hydrophobicity-based descriptor to characterize g14-3-3 client peptides. Finally, the X-ray structure of g14-3-3 in complex with a mode-1 prototype phosphopeptide was solved and combined with structure-based simulations to identify molecular features relevant for clients binding to g14-3-3. The data presented herein provide a further and structural understanding of g14-3-3 features and set the basis for drug design studies.
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Affiliation(s)
- Ylenia Cau
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , via Aldo Moro 2, 53019 Siena, Italy
| | - Annarita Fiorillo
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma , Piazzale A. Moro 5, 00185 Roma, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , via Aldo Moro 2, 53019 Siena, Italy.,Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia , Viale Regina Elena 291, 00161 Roma, Italy
| | - Andrea Ilari
- CNR-Institute of Molecular Biology and Pathology (IBPM), c/o Department Biochemical Sciences "A. Rossi Fanelli", University Sapienza , P.le A. Moro 5, 00185 Roma, Italy
| | - Maurizo Botta
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena , via Aldo Moro 2, 53019 Siena, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University , BioLife Science Building, Suite 333, 1900 North 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Marco Lalle
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità , Viale Regina Elena 299, 00161 Roma, Italy
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Molecular dynamic simulation insights into the normal state and restoration of p53 function. Int J Mol Sci 2012; 13:9709-9740. [PMID: 22949826 PMCID: PMC3431824 DOI: 10.3390/ijms13089709] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/06/2012] [Accepted: 07/11/2012] [Indexed: 12/13/2022] Open
Abstract
As a tumor suppressor protein, p53 plays a crucial role in the cell cycle and in cancer prevention. Almost 50 percent of all human malignant tumors are closely related to a deletion or mutation in p53. The activity of p53 is inhibited by over-active celluar antagonists, especially by the over-expression of the negative regulators MDM2 and MDMX. Protein-protein interactions, or post-translational modifications of the C-terminal negative regulatory domain of p53, also regulate its tumor suppressor activity. Restoration of p53 function through peptide and small molecular inhibitors has become a promising strategy for novel anti-cancer drug design and development. Molecular dynamics simulations have been extensively applied to investigate the conformation changes of p53 induced by protein-protein interactions and protein-ligand interactions, including peptide and small molecular inhibitors. This review focuses on the latest MD simulation research, to provide an overview of the current understanding of interactions between p53 and its partners at an atomic level.
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Allen WJ, Capelluto DGS, Finkielstein CV, Bevan DR. Modeling the relationship between the p53 C-terminal domain and its binding partners using molecular dynamics. J Phys Chem B 2011; 114:13201-13. [PMID: 20873738 DOI: 10.1021/jp1011445] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Fifty percent of all cancer cases result from mutations of the TP53 gene, which encodes the tumor suppressor p53, and it is hypothesized that the p53-mediated checkpoint pathway is compromised in most of the remaining cases. The p53 C-terminal domain (CTD) is an important site of p53 regulation but by nature is difficult to study, as it is intrinsically disordered. In this study, we performed molecular dynamics simulations on the p53 CTD and five known regulatory binding partners. We identified distinct trends in fluctuation within and around the p53 CTD binding site on each partner demonstrating a behavior that facilitates association. Further, we present evidence that the size of the hydrophobic pocket in each p53 CTD binding site governs the secondary structure of the p53 CTD when in the bound state. This information will be useful for predicting new binding partners for the p53 CTD, identifying interacting regions within other known partners, and discovering inhibitors that provide additional points of control over p53 activity.
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Affiliation(s)
- William J Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, 111 Engel Hall (0308), Blacksburg, Virginia 24061, United States
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Abstract
Pentamidine is a small molecule inhibitor of the Ca(+)-binding protein S100B and disrupts the S100B-p53 protein-protein interaction; this is thought to restore wild-type p53 tumour suppressor function in melanoma. Additional anticancer effects may be the result of inhibition of regenerating liver family phosphatases. In this study, we have used a standardized ATP-tumour chemosensitivity assay to investigate the effect of pentamidine on cells derived from 18 skin melanoma samples and one uveal melanoma sample. The cells were tested at six concentrations from which the IC(50) and IC(90) were calculated. To allow comparison between samples, an index(sum) was calculated based on the percentage of tumour growth inhibition at each concentration. Of the skin melanoma samples tested, 78% exhibited an index(sum) less than 300 indicating strong inhibition. The median index(sum) of 237 also indicates considerable activity against these samples. The median IC(90) (30.2 micromol/l) may be clinically achievable in a proportion of patients. The uveal melanoma sample exhibited an index(sum) of 333 indicating moderate inhibition, and 86% inhibition at test drug concentration (37.96 micromol/l). These results show that pentamidine has activity against melanoma, and support the prospect of its development for therapeutic use.
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