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Bojarski KK, David A, Lecaille F, Samsonov SA. In silico approaches for better understanding cysteine cathepsin-glycosaminoglycan interactions. Carbohydr Res 2024; 543:109201. [PMID: 39013335 DOI: 10.1016/j.carres.2024.109201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/18/2024]
Abstract
Cysteine cathepsins constitute the largest cathepsin family, with 11 proteases in human that are present primarily within acidic endosomal and lysosomal compartments. They are involved in the turnover of intracellular and extracellular proteins. They are synthesized as inactive procathepsins that are converted to mature active forms. Cathepsins play important roles in physiological and pathological processes and, therefore, receive increasing attention as potential therapeutic targets. Their maturation and activity can be regulated by glycosaminoglycans (GAGs), long linear negatively charged polysaccharides composed of recurring dimeric units. In this review, we summarize recent computational progress in the field of (pro)cathepsin-GAG complexes analyses.
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Affiliation(s)
- Krzysztof K Bojarski
- Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, Gdansk, 80-233, Poland.
| | - Alexis David
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes Protéolytiques dans l'Inflammation, Tours, France
| | - Fabien Lecaille
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes Protéolytiques dans l'Inflammation, Tours, France
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
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2
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Yan SW, Cheng YK, Lu QQ, Zhang R, Dan Liu R, Long SR, Wang ZQ, Cui J. Characterization of a novel dipeptidyl peptidase 1 of Trichinella spiralis and its participation in larval invasion. Acta Trop 2024; 249:107076. [PMID: 37977254 DOI: 10.1016/j.actatropica.2023.107076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/19/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
The research aimed to describe a new Trichinella spiralis dipeptidyl peptidase 1 (TsDPP1) and investigate its functions in the larval invasion of intestinal epithelial cells (IECs). The gene TsDPP1 was successfully replicated and produced in Escherichia coli BL21 (DE3), showing a strong immune response. TsDPP1 was detected in diverse stages of T. spiralis and showed significant expression in the intestine infective larvae (IIL) and adult worms at 6 days post infection, as confirmed by qPCR and Western blot analysis. The primary localization of TsDPP1 in this parasite was observed in cuticles, stichosomes, and embryos by using the indirect immunofluorescence assay (IIFA). rTsDPP1 exhibited the enzymatic function of natural dipeptidyl peptidase and showed specific binding to IECs, and the binding site was found to be localized on cell membrane. Following transfection with dsRNA-TsDPP1, the expression of TsDPP1 mRNA and protein in muscle larvae (ML) were decreased by approximately 63.52 % and 58.68 %, correspondingly. The activity of TsDPP1 in the ML and IIL treated with dsRNA-TsDPP1 was reduced by 42.98 % and 45.07 %, respectively. The acceleration of larval invasion of IECs was observed with rTsDPP1, while the invasion was suppressed by anti-rTsDPP1 serum. The ability of the larvae treated with dsRNA-TsDPP1 to invade IECs was hindered by 31.23 %. In mice infected with dsRNA-treated ML, the intestinal IIL, and adults experienced a significant decrease in worm burdens and a noticeable reduction in adult female length and fecundity compared to the PBS group. These findings indicated that TsDPP1 significantly impedes the invasion, growth, and reproductive capacity of T. spiralis in intestines, suggesting its potential as a target for anti-Trichinella vaccines.
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Affiliation(s)
- Shu Wei Yan
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, PR China
| | - Yong Kang Cheng
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, PR China
| | - Qi Qi Lu
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, PR China
| | - Ru Zhang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, PR China
| | - Ruo Dan Liu
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, PR China
| | - Shao Rong Long
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, PR China
| | - Zhong Quan Wang
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, PR China.
| | - Jing Cui
- Department of Parasitology, Medical College, Zhengzhou University, Zhengzhou, 450052, PR China.
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3
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Hua J, Garcia de Paco E, Linck N, Maurice T, Desrumaux C, Manoury B, Rassendren F, Ulmann L. Microglial P2X4 receptors promote ApoE degradation and contribute to memory deficits in Alzheimer's disease. Cell Mol Life Sci 2023; 80:138. [PMID: 37145189 PMCID: PMC10163120 DOI: 10.1007/s00018-023-04784-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023]
Abstract
Numerous evidences support that microglia contributes to the progression of Alzheimer's disease. P2X4 receptors are ATP-gated channels with high calcium permeability, which are de novo expressed in a subset of reactive microglia associated with various pathological contexts, contributing to microglial functions. P2X4 receptors are mainly localized in lysosomes and trafficking to the plasma membrane is tightly regulated. Here, we investigated the role of P2X4 in the context of Alzheimer's disease (AD). Using proteomics, we identified Apolipoprotein E (ApoE) as a specific P2X4 interacting protein. We found that P2X4 regulates lysosomal cathepsin B (CatB) activity promoting ApoE degradation; P2rX4 deletion results in higher amounts of intracellular and secreted ApoE in both bone-marrow-derived macrophage (BMDM) and microglia from APPswe/PSEN1dE9 brain. In both human AD brain and APP/PS1 mice, P2X4 and ApoE are almost exclusively expressed in plaque-associated microglia. In 12-month-old APP/PS1 mice, genetic deletion of P2rX4 reverses topographical and spatial memory impairment and reduces amount of soluble small aggregates of Aß1-42 peptide, while no obvious alteration of plaque-associated microglia characteristics is observed. Our results support that microglial P2X4 promotes lysosomal ApoE degradation, indirectly altering Aß peptide clearance, which in turn might promotes synaptic dysfunctions and cognitive deficits. Our findings uncover a specific interplay between purinergic signaling, microglial ApoE, soluble Aß (sAß) species and cognitive deficits associated with AD.
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Affiliation(s)
- Jennifer Hua
- IGF, Univ Montpellier, CNRS, INSERM, Montpellier, France
- LabEx Ion Channel Science and Therapeutics, Montpellier, France
| | - Elvira Garcia de Paco
- IGF, Univ Montpellier, CNRS, INSERM, Montpellier, France
- LabEx Ion Channel Science and Therapeutics, Montpellier, France
| | - Nathalie Linck
- IGF, Univ Montpellier, CNRS, INSERM, Montpellier, France
- LabEx Ion Channel Science and Therapeutics, Montpellier, France
| | - Tangui Maurice
- MMDN, Univ Montpellier, EPHE, INSERM, Montpellier, France
| | | | - Bénédicte Manoury
- Institut Necker Enfants Malades, INSERM, CNRS, Université de Paris, Paris, France
| | - François Rassendren
- IGF, Univ Montpellier, CNRS, INSERM, Montpellier, France
- LabEx Ion Channel Science and Therapeutics, Montpellier, France
| | - Lauriane Ulmann
- IGF, Univ Montpellier, CNRS, INSERM, Montpellier, France.
- LabEx Ion Channel Science and Therapeutics, Montpellier, France.
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4
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Berg AL, Rowson-Hodel A, Wheeler MR, Hu M, Free SR, Carraway KL. Engaging the Lysosome and Lysosome-Dependent Cell Death in Cancer. Breast Cancer 2022. [DOI: 10.36255/exon-publications-breast-cancer-lysosome] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Janke JJ, Yu Y, Pomin VH, Zhao J, Wang C, Linhardt RJ, García AE. Characterization of Heparin's Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy. J Chem Theory Comput 2022; 18:1894-1904. [PMID: 35108013 PMCID: PMC9027489 DOI: 10.1021/acs.jctc.1c00760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin's solution conformational dynamics and structure-function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule's underlying conformational ensemble, which then provides important information necessary for understanding structure-function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin's conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. The anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.
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Affiliation(s)
- J Joel Janke
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Yanlei Yu
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Vitor H Pomin
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Angel E García
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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Iverson E, Kaler L, Agostino EL, Song D, Duncan GA, Scull MA. Leveraging 3D Model Systems to Understand Viral Interactions with the Respiratory Mucosa. Viruses 2020; 12:E1425. [PMID: 33322395 PMCID: PMC7763686 DOI: 10.3390/v12121425] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/27/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023] Open
Abstract
Respiratory viruses remain a significant cause of morbidity and mortality in the human population, underscoring the importance of ongoing basic research into virus-host interactions. However, many critical aspects of infection are difficult, if not impossible, to probe using standard cell lines, 2D culture formats, or even animal models. In vitro systems such as airway epithelial cultures at air-liquid interface, organoids, or 'on-chip' technologies allow interrogation in human cells and recapitulate emergent properties of the airway epithelium-the primary target for respiratory virus infection. While some of these models have been used for over thirty years, ongoing advancements in both culture techniques and analytical tools continue to provide new opportunities to investigate airway epithelial biology and viral infection phenotypes in both normal and diseased host backgrounds. Here we review these models and their application to studying respiratory viruses. Furthermore, given the ability of these systems to recapitulate the extracellular microenvironment, we evaluate their potential to serve as a platform for studies specifically addressing viral interactions at the mucosal surface and detail techniques that can be employed to expand our understanding.
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Affiliation(s)
- Ethan Iverson
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA; (E.I.); (E.L.A.)
| | - Logan Kaler
- Biophysics Program, University of Maryland, College Park, MD 20742, USA; (L.K.); (G.A.D.)
| | - Eva L. Agostino
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA; (E.I.); (E.L.A.)
| | - Daniel Song
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA;
| | - Gregg A. Duncan
- Biophysics Program, University of Maryland, College Park, MD 20742, USA; (L.K.); (G.A.D.)
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA;
| | - Margaret A. Scull
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA; (E.I.); (E.L.A.)
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Schwenck J, Maurer A, Fehrenbacher B, Mehling R, Knopf P, Mucha N, Haupt D, Fuchs K, Griessinger CM, Bukala D, Holstein J, Schaller M, Menendez IG, Ghoreschi K, Quintanilla-Martinez L, Gütschow M, Laufer S, Reinheckel T, Röcken M, Kalbacher H, Pichler BJ, Kneilling M. Cysteine-type cathepsins promote the effector phase of acute cutaneous delayed-type hypersensitivity reactions. Theranostics 2019; 9:3903-3917. [PMID: 31281521 PMCID: PMC6587341 DOI: 10.7150/thno.31037] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 03/28/2019] [Indexed: 01/09/2023] Open
Abstract
Cysteine-type cathepsins such as cathepsin B are involved in various steps of inflammatory processes such as antigen processing and angiogenesis. Here, we uncovered the role of cysteine-type cathepsins in the effector phase of T cell-driven cutaneous delayed-type hypersensitivity reactions (DTHR) and the implication of this role on therapeutic cathepsin B-specific inhibition. Methods: Wild-type, cathepsin B-deficient (Ctsb-/-) and cathepsin Z-deficient (Ctsz-/-) mice were sensitized with 2,4,6-trinitrochlorobenzene (TNCB) on the abdomen and challenged with TNCB on the right ear to induce acute and chronic cutaneous DTHR. The severity of cutaneous DTHR was assessed by evaluating ear swelling responses and histopathology. We performed fluorescence microscopy on tissue from inflamed ears and lymph nodes of wild-type mice, as well as on biopsies from psoriasis patients, focusing on cathepsin B expression by T cells, B cells, macrophages, dendritic cells and NK cells. Cathepsin activity was determined noninvasively by optical imaging employing protease-activated substrate-like probes. Cathepsin expression and activity were validated ex vivo by covalent active site labeling of proteases and Western blotting. Results: Noninvasive in vivo optical imaging revealed strong cysteine-type cathepsin activity in inflamed ears and draining lymph nodes in acute and chronic cutaneous DTHR. In inflamed ears and draining lymph nodes, cathepsin B was expressed by neutrophils, dendritic cells, macrophages, B, T and natural killer (NK) cells. Similar expression patterns were found in psoriatic plaques of patients. The biochemical methods confirmed active cathepsin B in tissues of mice with cutaneous DTHR. Topically applied cathepsin B inhibitors significantly reduced ear swelling in acute but not chronic DTHR. Compared with wild-type mice, Ctsb-/- mice exhibited an enhanced ear swelling response during acute DTHR despite a lack of cathepsin B expression. Cathepsin Z, a protease closely related to cathepsin B, revealed compensatory expression in inflamed ears of Ctsb-/- mice, while cathepsin B expression was reciprocally elevated in Ctsz-/- mice. Conclusion: Cathepsin B is actively involved in the effector phase of acute cutaneous DTHR. Thus, topically applied cathepsin B inhibitors might effectively limit DTHR such as contact dermatitis or psoriasis. However, the cathepsin B and Z knockout mouse experiments suggested a complementary role for these two cysteine-type proteases.
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8
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Dissecting a novel allosteric mechanism of cruzain: A computer-aided approach. PLoS One 2019; 14:e0211227. [PMID: 30682119 PMCID: PMC6347273 DOI: 10.1371/journal.pone.0211227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/09/2019] [Indexed: 02/08/2023] Open
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, a neglected infection affecting millions of people in tropical regions. There are several chemotherapeutic agents for the treatment of this disease, but most of them are highly toxic and generate resistance. Currently, the development of allosteric inhibitors constitutes a promising research field, since it can improve the accessibility to more selective and less toxic medicines. To date, the allosteric drugs prediction is a state-of-the-art topic in rational structure-based computational design. In this work, a simulation strategy was developed for computational discovery of allosteric inhibitors, and it was applied to cruzain, a promising target and the major cysteine protease of T. cruzi. Molecular dynamics simulations, binding free energy calculations and network-based modelling of residue interactions were combined to characterize and compare molecular distinctive features of the apo form and the cruzain-allosteric inhibitor complexes. By using geometry-based criteria on trajectory snapshots, we predicted two main allosteric sites suitable for drug targeting. The results suggest dissimilar mechanisms exerted by the same allosteric site when binding different potential allosteric inhibitors. Finally, we identified the residues involved in suboptimal paths linking the identified site and the orthosteric site. The present study constitutes the first approximation to the design of cruzain allosteric inhibitors and may serve for future pharmacological intervention. Here, no major effects on active site structure were observed due to compound binding (modification of distance and angles between catalytic residues), which indicates that allosteric regulation in cruzain might be mediated via alterations of its dynamical properties similarly to allosteric inhibition of human cathepsin K (HCatK). The current findings are particularly relevant for the design of allosteric modulators of papain-like cysteine proteases.
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Patel S, Homaei A, El-Seedi HR, Akhtar N. Cathepsins: Proteases that are vital for survival but can also be fatal. Biomed Pharmacother 2018; 105:526-532. [PMID: 29885636 PMCID: PMC7172164 DOI: 10.1016/j.biopha.2018.05.148] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 12/27/2022] Open
Abstract
The state of enzymes in the human body determines the normal physiology or pathology, so all the six classes of enzymes are crucial. Proteases, the hydrolases, can be of several types based on the nucleophilic amino acid or the metal cofactor needed for their activity. Cathepsins are proteases with serine, cysteine, or aspartic acid residues as the nucleophiles, which are vital for digestion, coagulation, immune response, adipogenesis, hormone liberation, peptide synthesis, among a litany of other functions. But inflammatory state radically affects their normal roles. Released from the lysosomes, they degrade extracellular matrix proteins such as collagen and elastin, mediating parasite infection, autoimmune diseases, tumor metastasis, cardiovascular issues, and neural degeneration, among other health hazards. Over the years, the different types and isoforms of cathepsin, their optimal pH and functions have been studied, yet much information is still elusive. By taming and harnessing cathepsins, by inhibitors and judicious lifestyle, a gamut of malignancies can be resolved. This review discusses these aspects, which can be of clinical relevance.
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA,Corresponding author.
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran,Department of Biology, Faculty of Sciences, University of Hormozgan, Bandar Abbas, Iran
| | - Hesham R. El-Seedi
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Biomedical Centre, Box 574, SE-751 23, Uppsala, Sweden,Ecological Chemistry Group, Department of Chemistry, School of Chemical Science and Engineering, KTH, Stockholm, Sweden
| | - Nadeem Akhtar
- Department of Animal Biosciences, University of Guelph, Ontario, N1G 2W1, Canada
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Lang EJM, Heyes LC, Jameson GB, Parker EJ. Calculated pKa Variations Expose Dynamic Allosteric Communication Networks. J Am Chem Soc 2016; 138:2036-45. [DOI: 10.1021/jacs.5b13134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Geoffrey B. Jameson
- Institute
of Fundamental Sciences, Massey University, PO Box 11-222, Palmerston North 4422, New Zealand
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11
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A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods. Nat Commun 2015; 5:3287. [PMID: 24518821 DOI: 10.1038/ncomms4287] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 01/20/2014] [Indexed: 12/30/2022] Open
Abstract
Allosteric modifiers have the potential to fine-tune enzyme activity. Therefore, targeting allosteric sites is gaining increasing recognition as a strategy in drug design. Here we report the use of computational methods for the discovery of the first small-molecule allosteric inhibitor of the collagenolytic cysteine peptidase cathepsin K, a major target for the treatment of osteoporosis. The molecule NSC13345 is identified by high-throughput docking of compound libraries to surface sites on the peptidase that are connected to the active site by an evolutionarily conserved network of residues (protein sector). The crystal structure of the complex shows that NSC13345 binds to a novel allosteric site on cathepsin K. The compound acts as a hyperbolic mixed modifier in the presence of a synthetic substrate, it completely inhibits collagen degradation and has good selectivity for cathepsin K over related enzymes. Altogether, these properties qualify our methodology and NSC13345 as promising candidates for allosteric drug design.
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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Strumillo M, Beltrao P. Towards the computational design of protein post-translational regulation. Bioorg Med Chem 2015; 23:2877-82. [PMID: 25956846 PMCID: PMC4673319 DOI: 10.1016/j.bmc.2015.04.056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 12/19/2022]
Abstract
Protein post-translational modifications (PTMs) are a fast and versatility mechanism used by the cell to regulate the function of proteins in response to changing conditions. PTMs can alter the activity of proteins by allosteric regulation or by controlling protein interactions, localization and abundance. Recent advances in proteomics have revealed the extent of regulation by PTMs and the different mechanisms used in nature to exert control over protein function via PTMs. These developments can serve as the foundation for the rational design of protein regulation. Here we review the advances in methods to determine the function of PTMs, protein allosteric control and examples of rational design of PTM regulation. These advances create an opportunity to move synthetic biology forward by making use of a level of regulation that is of yet unexplored.
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Affiliation(s)
- Marta Strumillo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK; iBiMED and Department of Health Sciences, University of Aveiro, 3810-193 Aveiro, Portugal.
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14
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Cysteine cathepsin activity regulation by glycosaminoglycans. BIOMED RESEARCH INTERNATIONAL 2014; 2014:309718. [PMID: 25587532 PMCID: PMC4283429 DOI: 10.1155/2014/309718] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/02/2014] [Indexed: 11/26/2022]
Abstract
Cysteine cathepsins are a group of enzymes normally found in the endolysosomes where they are primarily involved in intracellular protein turnover but also have a critical role in MHC II-mediated antigen processing and presentation. However, in a number of pathologies cysteine cathepsins were found to be heavily upregulated and secreted into extracellular milieu, where they were found to degrade a number of extracellular proteins. A major role in modulating cathepsin activities play glycosaminoglycans, which were found not only to facilitate their autocatalytic activation including at neutral pH, but also to critically modulate their activities such as in the case of the collagenolytic activity of cathepsin K. The interaction between cathepsins and glycosaminoglycans will be discussed in more detail.
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15
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Costa MGS, Benetti-Barbosa TG, Desdouits N, Blondel A, Bisch PM, Pascutti PG, Batista PR. Impact of M36I polymorphism on the interaction of HIV-1 protease with its substrates: insights from molecular dynamics. BMC Genomics 2014; 15 Suppl 7:S5. [PMID: 25573486 PMCID: PMC4243740 DOI: 10.1186/1471-2164-15-s7-s5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Over the last decades, a vast structural knowledge has been gathered on the HIV-1 protease (PR). Noticeably, most of the studies focused the B-subtype, which has the highest prevalence in developed countries. Accordingly, currently available anti-HIV drugs target this subtype, with considerable benefits for the corresponding patients. However, in developing countries, there is a wide variety of HIV-1 subtypes carrying PR polymorphisms related to reduced drug susceptibility. The non-active site mutation, M36I, is the most frequent polymorphism, and is considered as a non-B subtype marker. Yet, the structural impact of this substitution on the PR structure and on the interaction with natural substrates remains poorly documented. Results Herein, we used molecular dynamics simulations to investigate the role of this polymorphism on the interaction of PR with six of its natural cleavage-sites substrates. Free energy analyses by MMPB/SA calculations showed an affinity decrease of M36I-PR for the majority of its substrates. The only exceptions were the RT-RH, with equivalent affinity, and the RH-IN, for which an increased affinity was found. Furthermore, molecular simulations suggest that, unlike other peptides, RH-IN induced larger structural fluctuations in the wild-type enzyme than in the M36I variant. Conclusions With multiple approaches and analyses we identified structural and dynamical determinants associated with the changes found in the binding affinity of the M36I variant. This mutation influences the flexibility of both PR and its complexed substrate. The observed impact of M36I, suggest that combination with other non-B subtype polymorphisms, could lead to major effects on the interaction with the 12 known cleavage sites, which should impact the virion maturation.
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Theoretical insight into the mechanism for the inhibition of the cysteine protease cathepsin B by 1,2,4-thiadiazole derivatives. J Mol Model 2014; 20:2254. [DOI: 10.1007/s00894-014-2254-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022]
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Agostino M, Gandhi NS, Mancera RL. Development and application of site mapping methods for the design of glycosaminoglycans. Glycobiology 2014; 24:840-51. [DOI: 10.1093/glycob/cwu045] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Yoneyama S, Guo Y, Lanktree MB, Barnes MR, Elbers CC, Karczewski KJ, Padmanabhan S, Bauer F, Baumert J, Beitelshees A, Berenson GS, Boer JM, Burke G, Cade B, Chen W, Cooper-Dehoff RM, Gaunt TR, Gieger C, Gong Y, Gorski M, Heard-Costa N, Johnson T, Lamonte MJ, Mcdonough C, Monda KL, Onland-Moret NC, Nelson CP, O'Connell JR, Ordovas J, Peter I, Peters A, Shaffer J, Shen H, Smith E, Speilotes L, Thomas F, Thorand B, Monique Verschuren WM, Anand SS, Dominiczak A, Davidson KW, Hegele RA, Heid I, Hofker MH, Huggins GS, Illig T, Johnson JA, Kirkland S, König W, Langaee TY, Mccaffery J, Melander O, Mitchell BD, Munroe P, Murray SS, Papanicolaou G, Redline S, Reilly M, Samani NJ, Schork NJ, Van Der Schouw YT, Shimbo D, Shuldiner AR, Tobin MD, Wijmenga C, Yusuf S, Hakonarson H, Lange LA, Demerath EW, Fox CS, North KE, Reiner AP, Keating B, Taylor KC. Gene-centric meta-analyses for central adiposity traits in up to 57 412 individuals of European descent confirm known loci and reveal several novel associations. Hum Mol Genet 2014; 23:2498-510. [PMID: 24345515 PMCID: PMC3988452 DOI: 10.1093/hmg/ddt626] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 11/18/2013] [Accepted: 12/09/2013] [Indexed: 12/15/2022] Open
Abstract
Waist circumference (WC) and waist-to-hip ratio (WHR) are surrogate measures of central adiposity that are associated with adverse cardiovascular events, type 2 diabetes and cancer independent of body mass index (BMI). WC and WHR are highly heritable with multiple susceptibility loci identified to date. We assessed the association between SNPs and BMI-adjusted WC and WHR and unadjusted WC in up to 57 412 individuals of European descent from 22 cohorts collaborating with the NHLBI's Candidate Gene Association Resource (CARe) project. The study population consisted of women and men aged 20-80 years. Study participants were genotyped using the ITMAT/Broad/CARE array, which includes ∼50 000 cosmopolitan tagged SNPs across ∼2100 cardiovascular-related genes. Each trait was modeled as a function of age, study site and principal components to control for population stratification, and we conducted a fixed-effects meta-analysis. No new loci for WC were observed. For WHR analyses, three novel loci were significantly associated (P < 2.4 × 10(-6)). Previously unreported rs2811337-G near TMCC1 was associated with increased WHR (β ± SE, 0.048 ± 0.008, P = 7.7 × 10(-9)) as was rs7302703-G in HOXC10 (β = 0.044 ± 0.008, P = 2.9 × 10(-7)) and rs936108-C in PEMT (β = 0.035 ± 0.007, P = 1.9 × 10(-6)). Sex-stratified analyses revealed two additional novel signals among females only, rs12076073-A in SHC1 (β = 0.10 ± 0.02, P = 1.9 × 10(-6)) and rs1037575-A in ATBDB4 (β = 0.046 ± 0.01, P = 2.2 × 10(-6)), supporting an already established sexual dimorphism of central adiposity-related genetic variants. Functional analysis using ENCODE and eQTL databases revealed that several of these loci are in regulatory regions or regions with differential expression in adipose tissue.
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Affiliation(s)
| | - Yiran Guo
- Center for Applied Genomics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Abramson Research Center, Philadelphia, PA 19104, USA
- BGI-Shenzhen, Beishan Beishan Industrial Zone,Yantian District, Shenzhen 518083, China
| | | | - Michael R. Barnes
- National Institute for Health Biomedical Research Unit
- London School of Medicine
| | - Clara C. Elbers
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
| | | | | | - Florianne Bauer
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
| | | | | | - Gerald S. Berenson
- Department of Epidemiology, Tulane University, New Orleans, LA 70112, USA
| | - Jolanda M.A. Boer
- Center for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | | | - Brian Cade
- Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
- Division of Sleep Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Wei Chen
- Department of Epidemiology, Tulane University, New Orleans, LA 70112, USA
| | - Rhonda M. Cooper-Dehoff
- Department of Pharmacotherapy and Translational Research
- Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, Bristol BS8 2BN, UK
| | | | - Yan Gong
- Department of Pharmacotherapy and Translational Research
- Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Mathias Gorski
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, 93053 Regensburg, Germany
- Department of Internal Medicine II, University Medical Center Regensburg, 93053 Regensburg, Germany
| | | | - Toby Johnson
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts
- London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Michael J. Lamonte
- Department of Social and Preventive Medicine, SUNY-Buffalo School of Public Health and Health Professions, Buffalo, NY 14214, USA
| | - Caitrin Mcdonough
- Department of Pharmacotherapy and Translational Research
- Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Keri L. Monda
- Gillings School of Global Public Health
- The Center for Observational Research, Amgen, Inc., Thousand Oaks, CA 91320, USA
| | - N. Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Christopher P. Nelson
- Department of Cardiovascular Science, University of Leicester, Leicester LE3 9QP, UK
- Leicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester LE3 9QP, UK
| | | | - Jose Ordovas
- Nutrition and Genomics Laboratory, Tufts University, Boston, MA 02111, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jonathan Shaffer
- Division of General Medicine, Center for Behavioral Cardiovascular Health, Columbia University Medical Center, New York, NY 10032, USA
| | | | - Erin Smith
- Department of Pediatrics and Rady's Children's Hospital, University of California at San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Liz Speilotes
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Internal Medicine, Division of Gastroenterology
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- The Broad Institute, Cambridge, MA 02141, USA
| | - Fridtjof Thomas
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | | | - W. M. Monique Verschuren
- Center for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - Sonia S. Anand
- Population Health Research Institute, Hamilton Health Sciences, Department of Medicine, and
- Population Genomics Program, Department of Clinical Epidemiology, McMaster University, Hamilton, ON, CanadaL8S4L8
| | - Anna Dominiczak
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Karina W. Davidson
- Division of General Medicine, Center for Behavioral Cardiovascular Health, Columbia University Medical Center, New York, NY 10032, USA
| | - Robert A. Hegele
- Robarts Research Institute, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, CanadaN6A 5C1
| | - Iris Heid
- Institute of Genetic Epidemiology
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, 93053 Regensburg, Germany
| | - Marten H. Hofker
- Department of Molecular Genetics, University Medical Center Groningen, Groningen University, 9700 AB Groningen, The Netherlands
| | - Gordon S. Huggins
- Center for Translational Genomics, Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
| | - Thomas Illig
- Research Unit for Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, 30625 Hannover, Germany
| | - Julie A. Johnson
- Department of Pharmacotherapy and Translational Research
- Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Susan Kirkland
- Department of Community Health & Epidemiology, Dalhousie University, Halifax, NS, Canada
| | | | - Wolfgang König
- Department of Internal Medicine II, Cardiology, University of Ulm Medical Center, Ulm 89081, Germany
| | - Taimour Y. Langaee
- Department of Pharmacotherapy and Translational Research
- Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Jeanne Mccaffery
- Weight Control and Diabetes Research Center, The Miriam Hospital and
- Warren Alpert School of Medicine at Brown University, Providence, RI 02906, USA
| | - Olle Melander
- Department of Clinical Sciences, Hypertension & Cardiovascular Disease, Lund University, SE 20502 Malmo, Sweden
| | | | - Patricia Munroe
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts
- London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Sarah S. Murray
- The Scripps Research Institute, Scripps Health, La Jolla, CA 92037, USA
| | - George Papanicolaou
- Division of Prevention and Population Sciences, NHLBI, NIH, Bethesda, MD 20824, USA
| | - Susan Redline
- Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
- Division of Sleep Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Muredach Reilly
- Cardiovascular Institute, University of Pennsylvania Medical Center, Philadelphia, PA 19104, USA
| | - Nilesh J. Samani
- Department of Cardiovascular Science, University of Leicester, Leicester LE3 9QP, UK
- Leicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Nicholas J. Schork
- The Scripps Research Institute, Scripps Health, La Jolla, CA 92037, USA
- Scripps Translational Science Institute, La Jolla, CA 92037, USA
| | - Yvonne T. Van Der Schouw
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Daichi Shimbo
- Division of General Medicine, Center for Behavioral Cardiovascular Health, Columbia University Medical Center, New York, NY 10032, USA
| | - Alan R. Shuldiner
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Martin D. Tobin
- Department of Health Sciences
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, The Netherlands
| | - Salim Yusuf
- Population Health Research Institute, Hamilton Health Sciences, Department of Medicine, and
- Population Genomics Program, Department of Clinical Epidemiology, McMaster University, Hamilton, ON, CanadaL8S4L8
| | | | | | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Abramson Research Center, Philadelphia, PA 19104, USA
| | - Leslie A. Lange
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN 55454, USA
| | - Caroline S. Fox
- Framingham Heart Study, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kari E North
- Gillings School of Global Public Health
- Carolina Center for Genome Sciences, Chapel Hill, NC 27599, USA
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA 98195, USA
| | - Brendan Keating
- Center for Applied Genomics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Abramson Research Center, Philadelphia, PA 19104, USA
| | - Kira C. Taylor
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, Louisville, KY 40202, USA
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Zhang G, Morin C, Zhu X, Bao Huynh M, Ouidir Ouidja M, Sepulveda-Diaz JE, Raisman-Vozari R, Li P, Papy-Garcia D. Self-evolving oxidative stress with identifiable pre- and postmitochondrial phases in PC12 cells. J Neurosci Res 2012; 91:273-84. [DOI: 10.1002/jnr.23146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 07/25/2012] [Accepted: 08/25/2012] [Indexed: 11/10/2022]
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Bitar M, Drummond MG, Costa MGS, Lobo FP, Calzavara-Silva CE, Bisch PM, Machado CR, Macedo AM, Pierce RJ, Franco GR. Modeling the zing finger protein SmZF1 from Schistosoma mansoni: Insights into DNA binding and gene regulation. J Mol Graph Model 2012; 39:29-38. [PMID: 23220279 DOI: 10.1016/j.jmgm.2012.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/09/2012] [Accepted: 10/13/2012] [Indexed: 10/27/2022]
Abstract
Zinc finger proteins are widely found in eukaryotes, representing an important class of DNA-binding proteins frequently involved in transcriptional regulation. Zinc finger motifs are composed by two antiparallel β-strands and one α-helix, stabilized by a zinc ion coordinated by conserved histidine and cysteine residues. In Schistosoma mansoni, these regulatory proteins are known to modulate morphological and physiological changes, having crucial roles in parasite development. A previously described C(2)H(2) zinc finger protein, SmZF1, was shown to be present in cell nuclei of different life stages of S. mansoni and to activate gene transcription in a heterologous system. A high-quality SmZF1 tridimensional structure was generated using comparative modeling. Molecular dynamics simulations of the obtained structure revealed stability of the zinc fingers motifs and high flexibility on the terminals, comparable to the profile observed on the template X-ray structure based on thermal b-factors. Based on the protein tridimensional features and amino acid composition, we were able to characterize four C(2)H(2) zinc finger motifs, the first involved in protein-protein interactions while the three others involved in DNA binding. We defined a consensus DNA binding sequence using three distinct algorithms and further carried out docking calculations, which revealed the interaction of fingers 2-4 with the predicted DNA. A search for S. mansoni genes presenting putative SmZF1 binding sites revealed 415 genes hypothetically under SmZF1 control. Using an automatic annotation and GO assignment approach, we found that the majority of those genes code for proteins involved in developmental processes. Taken together, these results present a consistent base to the structural and functional characterization of SmZF1.
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Affiliation(s)
- Mainá Bitar
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Da Rocha Pita SS, Batista PR, Albuquerque MG, Pascutti PG. Molecular Dynamics Simulations of Peptide Inhibitors Complexed WithTrypanosoma cruziTrypanothione Reductase. Chem Biol Drug Des 2012; 80:561-71. [DOI: 10.1111/j.1747-0285.2012.01429.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Costa TF, Reis FCD, Lima APC. Substrate inhibition and allosteric regulation by heparan sulfate of Trypanosoma brucei cathepsin L. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:493-501. [DOI: 10.1016/j.bbapap.2011.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Revised: 12/13/2011] [Accepted: 12/23/2011] [Indexed: 11/27/2022]
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Cysteine cathepsins: from structure, function and regulation to new frontiers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:68-88. [PMID: 22024571 PMCID: PMC7105208 DOI: 10.1016/j.bbapap.2011.10.002] [Citation(s) in RCA: 878] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/03/2011] [Accepted: 10/04/2011] [Indexed: 02/06/2023]
Abstract
It is more than 50 years since the lysosome was discovered. Since then its hydrolytic machinery, including proteases and other hydrolases, has been fairly well identified and characterized. Among these are the cysteine cathepsins, members of the family of papain-like cysteine proteases. They have unique reactive-site properties and an uneven tissue-specific expression pattern. In living organisms their activity is a delicate balance of expression, targeting, zymogen activation, inhibition by protein inhibitors and degradation. The specificity of their substrate binding sites, small-molecule inhibitor repertoire and crystal structures are providing new tools for research and development. Their unique reactive-site properties have made it possible to confine the targets simply by the use of appropriate reactive groups. The epoxysuccinyls still dominate the field, but now nitriles seem to be the most appropriate “warhead”. The view of cysteine cathepsins as lysosomal proteases is changing as there is now clear evidence of their localization in other cellular compartments. Besides being involved in protein turnover, they build an important part of the endosomal antigen presentation. Together with the growing number of non-endosomal roles of cysteine cathepsins is growing also the knowledge of their involvement in diseases such as cancer and rheumatoid arthritis, among others. Finally, cysteine cathepsins are important regulators and signaling molecules of an unimaginable number of biological processes. The current challenge is to identify their endogenous substrates, in order to gain an insight into the mechanisms of substrate degradation and processing. In this review, some of the remarkable advances that have taken place in the past decade are presented. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
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Batista PR, Pandey G, Pascutti PG, Bisch PM, Perahia D, Robert CH. Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening. J Chem Theory Comput 2011; 7:2348-52. [PMID: 26606609 DOI: 10.1021/ct200237u] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Describing biological macromolecular energetics from computer simulations can pose major challenges, and often necessitates enhanced conformational sampling. We describe the calculation of conformational free-energy profiles along carefully chosen collective coordinates: "consensus" normal modes, developed recently as robust alternatives to conventional normal modes. In an application to the HIV-1 protease, we obtain efficient sampling of significant flap opening movements governing inhibitor binding from relatively short simulations, in close correspondence with experimental results.
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Affiliation(s)
- Paulo R Batista
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil.,CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.,CNRS BIMoDyM -Laboratoire de Biologie et Pharmacologie Appliquées - École Normale Supérieure de Cachan , 94235 Cachan, France
| | - Gaurav Pandey
- Indian Institute of Technology , Roorkee, 247667, India.,CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France
| | - Pedro G Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil
| | - Paulo M Bisch
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , 21941-902, Brasil
| | - David Perahia
- CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.,CNRS BIMoDyM -Laboratoire de Biologie et Pharmacologie Appliquées - École Normale Supérieure de Cachan , 94235 Cachan, France
| | - Charles H Robert
- CNRS Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université Paris Sud 11 , 91405 Orsay, France.,CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico Chimique, Université Paris Diderot, Sorbonne Paris Cité , 75005 Paris, France
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