1
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Gorantla KR, Krishnan A, Waheed SO, Varghese A, DiCastri I, LaRouche C, Paik M, Fields GB, Karabencheva-Christova TG. Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase-1. Biochemistry 2024. [PMID: 38963231 DOI: 10.1021/acs.biochem.4c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Collagen hydrolysis, catalyzed by Zn(II)-dependent matrix metalloproteinases (MMPs), is a critical physiological process. Despite previous computational investigations into the catalytic mechanisms of MMP-mediated collagenolysis, a significant knowledge gap in understanding remains regarding the influence of conformational sampling and entropic contributions at physiological temperature on enzymatic collagenolysis. In our comprehensive multilevel computational study, employing quantum mechanics/molecular mechanics (QM/MM) metadynamics (MetD) simulations, we aimed to bridge this gap and provide valuable insights into the catalytic mechanism of MMP-1. Specifically, we compared the full enzyme-substrate complex in solution, clusters in solution, and gas-phase to elucidate insights into MMP-1-catalyzed collagenolysis. Our findings reveal significant differences in the catalytic mechanism when considering thermal effects and the dynamic evolution of the system, contrasting with conventional static potential energy surface QM/MM reaction path studies. Notably, we observed a significant stabilization of the critical tetrahedral intermediate, attributed to contributions from conformational flexibility and entropy. Moreover, we found that protonation of the scissile bond nitrogen occurs via proton transfer from a Zn(II)-coordinated hydroxide rather than from a solvent water molecule. Following C-N bond cleavage, the C-terminus remains coordinated to the catalytic Zn(II), while the N-terminus forms a hydrogen bond with a solvent water molecule. Subsequently, the release of the C-terminus is facilitated by the coordination of a water molecule. Our study underscores the pivotal role of protein conformational dynamics at physiological temperature in stabilizing the transition state of the rate-limiting step and key intermediates, compared to the corresponding reaction in solution. These fundamental insights into the mechanism of collagen degradation provide valuable guidance for the development of MMP-1-specific inhibitors.
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Affiliation(s)
- Koteswara Rao Gorantla
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Anandhu Krishnan
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ann Varghese
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Isabella DiCastri
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ciara LaRouche
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Meredith Paik
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Gregg B Fields
- Department of Chemistry and Biochemistry and I-HEALTH, Florida Atlantic University, Jupiter, Florida 33458, United States
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2
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Bui TM, Yalom LK, Ning E, Urbanczyk JM, Ren X, Herrnreiter CJ, Disario JA, Wray B, Schipma MJ, Velichko YS, Sullivan DP, Abe K, Lauberth SM, Yang GY, Dulai PS, Hanauer SB, Sumagin R. Tissue-specific reprogramming leads to angiogenic neutrophil specialization and tumor vascularization in colorectal cancer. J Clin Invest 2024; 134:e174545. [PMID: 38329810 PMCID: PMC10977994 DOI: 10.1172/jci174545] [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: 08/04/2023] [Accepted: 02/06/2024] [Indexed: 02/10/2024] Open
Abstract
Neutrophil (PMN) tissue accumulation is an established feature of ulcerative colitis (UC) lesions and colorectal cancer (CRC). To assess the PMN phenotypic and functional diversification during the transition from inflammatory ulceration to CRC we analyzed the transcriptomic landscape of blood and tissue PMNs. Transcriptional programs effectively separated PMNs based on their proximity to peripheral blood, inflamed colon, and tumors. In silico pathway overrepresentation analysis, protein-network mapping, gene signature identification, and gene-ontology scoring revealed unique enrichment of angiogenic and vasculature development pathways in tumor-associated neutrophils (TANs). Functional studies utilizing ex vivo cultures, colitis-induced murine CRC, and patient-derived xenograft models demonstrated a critical role for TANs in promoting tumor vascularization. Spp1 (OPN) and Mmp14 (MT1-MMP) were identified by unbiased -omics and mechanistic studies to be highly induced in TANs, acting to critically regulate endothelial cell chemotaxis and branching. TCGA data set and clinical specimens confirmed enrichment of SPP1 and MMP14 in high-grade CRC but not in patients with UC. Pharmacological inhibition of TAN trafficking or MMP14 activity effectively reduced tumor vascular density, leading to CRC regression. Our findings demonstrate a niche-directed PMN functional specialization and identify TAN contributions to tumor vascularization, delineating what we believe to be a new therapeutic framework for CRC treatment focused on TAN angiogenic properties.
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Affiliation(s)
- Triet M. Bui
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lenore K. Yalom
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Edward Ning
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jessica M. Urbanczyk
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xingsheng Ren
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Caroline J. Herrnreiter
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jackson A. Disario
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Brian Wray
- Quantitative Data Science Core, Lurie Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Matthew J. Schipma
- Quantitative Data Science Core, Lurie Cancer Center, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Yuri S. Velichko
- Department of Radiology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - David P. Sullivan
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kouki Abe
- Simpson Querrey Institute for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shannon M. Lauberth
- Simpson Querrey Institute for Epigenetics and Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Guang-Yu Yang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Parambir S. Dulai
- Department of Medicine, Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, Illinois, USA
| | - Stephen B. Hanauer
- Department of Medicine, Gastroenterology and Hepatology, Northwestern Memorial Hospital, Chicago, Illinois, USA
| | - Ronen Sumagin
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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3
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Obaha A, Novinec M. Regulation of Peptidase Activity beyond the Active Site in Human Health and Disease. Int J Mol Sci 2023; 24:17120. [PMID: 38069440 PMCID: PMC10707025 DOI: 10.3390/ijms242317120] [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: 11/17/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
This comprehensive review addresses the intricate and multifaceted regulation of peptidase activity in human health and disease, providing a comprehensive investigation that extends well beyond the boundaries of the active site. Our review focuses on multiple mechanisms and highlights the important role of exosites, allosteric sites, and processes involved in zymogen activation. These mechanisms play a central role in shaping the complex world of peptidase function and are promising potential targets for the development of innovative drugs and therapeutic interventions. The review also briefly discusses the influence of glycosaminoglycans and non-inhibitory binding proteins on enzyme activities. Understanding their role may be a crucial factor in the development of therapeutic strategies. By elucidating the intricate web of regulatory mechanisms that control peptidase activity, this review deepens our understanding in this field and provides a roadmap for various strategies to influence and modulate peptidase activity.
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Affiliation(s)
| | - Marko Novinec
- Faculty of Chemistry and Chemical Technology, Department of Chemistry and Biochemistry, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia;
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4
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Varghese A, Waheed SO, Gorantla K, DiCastri I, LaRouche C, Kaski B, Fields GB, Karabencheva-Christova TG. Catalytic Mechanism of Collagen Hydrolysis by Zinc(II)-Dependent Matrix Metalloproteinase-1. J Phys Chem B 2023; 127:9697-9709. [PMID: 37931179 PMCID: PMC10659029 DOI: 10.1021/acs.jpcb.3c04293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
Human matrix metalloproteinase-1 (MMP-1) is a zinc(II)-dependent enzyme that catalyzes collagenolysis. Despite the availability of extensive experimental data, the mechanism of MMP-1-catalyzed collagenolysis remains poorly understood due to the lack of experimental structure of a catalytically productive enzyme-substrate complex of MMP-1. In this study, we apply molecular dynamics and combined quantum mechanics/molecular mechanics to reveal the reaction mechanism of MMP-1 based on a computationally modeled structure of the catalytically competent complex of MMP-1 that contains a large triple-helical peptide substrate. Our proposed mechanism involves the participation of an auxiliary (second) water molecule (wat2) in addition to the zinc(II)-coordinated water (wat1). The reaction initiates through a proton transfer to Glu219, followed by a nucleophilic attack by a zinc(II)-coordinated hydroxide anion nucleophile at the carbonyl carbon of the scissile bond, leading to the formation of a tetrahedral intermediate (IM2). The process continues with a hydrogen-bond rearrangement to facilitate proton transfer from wat2 to the amide nitrogen of the scissile bond and, finally, C-N bond cleavage. The calculations indicate that the rate-determining step is the water-mediated nucleophilic attack with an activation energy barrier of 22.3 kcal/mol. Furthermore, the calculations show that the hydrogen-bond rearrangement/proton-transfer step can proceed in a consecutive or concerted manner, depending on the conformation of the tetrahedral intermediate, with the consecutive mechanism being energetically preferable. Overall, the study reveals the crucial role of a second water molecule and the dynamics for effective MMP-1-catalyzed collagenolysis.
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Affiliation(s)
- Ann Varghese
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Sodiq O. Waheed
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Koteswararao Gorantla
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Isabella DiCastri
- Department
of Chemical Engineering, Michigan Technological
University, Houghton, Michigan 49931, United States
| | - Ciara LaRouche
- Department
of Chemical Engineering, Michigan Technological
University, Houghton, Michigan 49931, United States
| | - Brendan Kaski
- Department
of Kinesiology and Integrative Physiology, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Gregg B. Fields
- Department
of Chemistry and Biochemistry and I-HEALTH, Florida Atlantic University, Jupiter, Florida 33458, United States
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5
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Structure of Vibrio collagenase VhaC provides insight into the mechanism of bacterial collagenolysis. Nat Commun 2022; 13:566. [PMID: 35091565 PMCID: PMC8799719 DOI: 10.1038/s41467-022-28264-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/10/2022] [Indexed: 02/06/2023] Open
Abstract
The collagenases of Vibrio species, many of which are pathogens, have been regarded as an important virulence factor. However, there is little information on the structure and collagenolytic mechanism of Vibrio collagenase. Here, we report the crystal structure of the collagenase module (CM) of Vibrio collagenase VhaC and the conformation of VhaC in solution. Structural and biochemical analyses and molecular dynamics studies reveal that triple-helical collagen is initially recognized by the activator domain, followed by subsequent cleavage by the peptidase domain along with the closing movement of CM. This is different from the peptidolytic mode or the proposed collagenolysis of Clostridium collagenase. We propose a model for the integrated collagenolytic mechanism of VhaC, integrating the functions of VhaC accessory domains and its collagen degradation pattern. This study provides insight into the mechanism of bacterial collagenolysis and helps in structure-based drug design targeting of the Vibrio collagenase. The collagenolytic mechanism of Vibrio collagenase, a virulence factor, remains unclear. Here, the authors report the structure of Vibrio collagenase VhaC and propose the mechanism for collagen recognition and degradation, providing new insight into bacterial collagenolysis.
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6
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Varghese A, Chaturvedi SS, Fields GB, Karabencheva-Christova TG. A synergy between the catalytic and structural Zn(II) ions and the enzyme and substrate dynamics underlies the structure-function relationships of matrix metalloproteinase collagenolysis. J Biol Inorg Chem 2021; 26:583-597. [PMID: 34228191 DOI: 10.1007/s00775-021-01876-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/28/2021] [Indexed: 10/20/2022]
Abstract
Matrix metalloproteinases (MMPs) are Zn(II) dependent endopeptidases involved in the degradation of collagen. Unbalanced collagen breakdown results in numerous pathological conditions, including cardiovascular and neurodegenerative diseases and tumor growth and invasion. Matrix metalloproteinase-1 (MMP-1) is a member of the MMPs family. The enzyme contains catalytic and structural Zn(II) ions. Despite many studies on the enzyme, there is little known about the synergy between the two Zn(II) metal ions and the enzyme and substrate dynamics in MMP-1 structure-function relationships. We performed a computational study of the MMP-1•triple-helical peptide (THP) enzyme•substrate complex to provide this missing insight. Our results revealed Zn(II) ions' importance in modulating the long-range correlated motions in the MMP-1•THP complex. Overall, our results reveal the importance of the catalytic Zn(II) and the role of the structural Zn(II) ion in preserving the integrity of the enzyme active site and the overall enzyme-substrate complex synergy with the dynamics of the enzyme and the substrate. Notably, both Zn(II) sites participate in diverse networks of long-range correlated motions that involve the CAT and HPX domains and the THP substrate, thus exercising a complex role in the stability and functionality of the MMP-1•THP complex. Both the Zn(II) ions have a distinct impact on the structural stability and dynamics of the MMP-1•THP complex. The study shifts the paradigm from the "local role" of the Zn(II) ions with knowledge about their essential role in the long-range dynamics and stability of the overall enzyme•substrate (ES) complex.
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Affiliation(s)
- Ann Varghese
- Department of Chemistry, Michigan Technological University, Houghton, MI, 49931, USA
| | - Shobhit S Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, MI, 49931, USA
| | - Gregg B Fields
- Department of Chemistry and Biochemistry and I-HEALTH, Florida Atlantic University, Jupiter, FL, 33458, USA
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7
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Kok HJ, Barton ER. Actions and interactions of IGF-I and MMPs during muscle regeneration. Semin Cell Dev Biol 2021; 119:11-22. [PMID: 33962867 DOI: 10.1016/j.semcdb.2021.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/04/2021] [Accepted: 04/19/2021] [Indexed: 12/11/2022]
Abstract
Muscle regeneration requires the coordination of several factors to mobilize satellite cells and macrophages, remodel the extracellular matrix surrounding muscle fibers, and repair existing and/or form new muscle fibers. In this review, we focus on insulin-like growth factor I and the matrix metalloproteinases, which are secreted proteins that act on cells and the matrix to resolve damage. While their actions appear independent, their interactions occur at the transcriptional and post-translational levels to promote feed-forward activation of each other. Together, these proteins assist at virtually every step of the repair process, and contribute significantly to muscle regenerative capacity.
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Affiliation(s)
- Hui Jean Kok
- Applied Physiology & Kinesiology, College of Health and Human Performance, University of Florida, 1864 Stadium Road, Gainesville, FL 32611, USA
| | - Elisabeth R Barton
- Applied Physiology & Kinesiology, College of Health and Human Performance, University of Florida, 1864 Stadium Road, Gainesville, FL 32611, USA.
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8
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Smith AJ, Alcock SG, Davidson LS, Emmins JH, Hiller Bardsley JC, Holloway P, Malfois M, Marshall AR, Pizzey CL, Rogers SE, Shebanova O, Snow T, Sutter JP, Williams EP, Terrill NJ. I22: SAXS/WAXS beamline at Diamond Light Source - an overview of 10 years operation. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:939-947. [PMID: 33950002 PMCID: PMC8127364 DOI: 10.1107/s1600577521002113] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/23/2021] [Indexed: 05/04/2023]
Abstract
Beamline I22 at Diamond Light Source is dedicated to the study of soft-matter systems from both biological and materials science. The beamline can operate in the range 3.7 keV to 22 keV for transmission SAXS and 14 keV to 20 keV for microfocus SAXS with beam sizes of 240 µm × 60 µm [full width half-maximum (FWHM) horizontal (H) × vertical (V)] at the sample for the main beamline, and approximately 10 µm × 10 µm for the dedicated microfocusing platform. There is a versatile sample platform for accommodating a range of facilities and user-developed sample environments. The high brilliance of the insertion device source on I22 allows structural investigation of materials under extreme environments (for example, fluid flow at high pressures and temperatures). I22 provides reliable access to millisecond data acquisition timescales, essential to understanding kinetic processes such as protein folding or structural evolution in polymers and colloids.
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Affiliation(s)
- A. J. Smith
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - S. G. Alcock
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - L. S. Davidson
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - J. H. Emmins
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - J. C. Hiller Bardsley
- King’s College London, Guy’s Campus, Great Maze Pond, London SE1 1UL, United Kingdom
| | - P. Holloway
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - M. Malfois
- ALBA Synchrotron, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain
| | - A. R. Marshall
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - C. L. Pizzey
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - S. E. Rogers
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - O. Shebanova
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - T. Snow
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - J. P. Sutter
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - E. P. Williams
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - N. J. Terrill
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
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9
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Manka SW, Brew K. Thermodynamic and Mechanistic Insights into Coupled Binding and Unwinding of Collagen by Matrix Metalloproteinase 1. J Mol Biol 2020; 432:5985-5993. [PMID: 33058879 DOI: 10.1016/j.jmb.2020.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/06/2020] [Accepted: 10/06/2020] [Indexed: 10/23/2022]
Abstract
Local unwinding of the collagen triple helix is a necessary step for initiating the collagen degradation cascade in extracellular matrices. A few matrix metalloproteinases (MMPs) are known to support this key process, but its energetic aspects remain unknown. Here, we captured the thermodynamics of the triple helix unwinding by monitoring interactions between a collagen peptide and MMP-1(E200A) - an active-site mutant of an archetypal vertebrate collagenase - at increasing temperatures, using isothermal titration calorimetry (ITC). Coupled binding and unwinding manifests as a curved relationship between the total enthalpy change and temperature of the reaction, producing increasingly negative heat capacity change (ΔΔCp ≈ -36.3 kcal/molK2). A specially designed solid-phase binding and cleavage assay (SPBCA) reported strain in the catalytically relevant unwound state, suggesting that this state is distinct from the horizon of sampled conformations of the collagenase-susceptible site. MMP-1 appears to blend selected fit with induced fit mechanisms to catalyse collagen unwinding prior to cleavage of individual collagen chains.
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Affiliation(s)
- Szymon W Manka
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
| | - Keith Brew
- Department of Biomedical Science, Florida Atlantic University, Boca Raton, FL 33431, USA
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10
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Kumar L, Nash A, Harms C, Planas-Iglesias J, Wright D, Klein-Seetharaman J, Sarkar SK. Allosteric Communications between Domains Modulate the Activity of Matrix Metalloprotease-1. Biophys J 2020; 119:360-374. [PMID: 32585130 PMCID: PMC7376139 DOI: 10.1016/j.bpj.2020.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/30/2020] [Accepted: 06/09/2020] [Indexed: 11/23/2022] Open
Abstract
An understanding of the structure-dynamics relationship is essential for understanding how a protein works. Prior research has shown that the activity of a protein correlates with intradomain dynamics occurring at picosecond to millisecond timescales. However, the correlation between interdomain dynamics and the function of a protein is poorly understood. Here, we show that communications between the catalytic and hemopexin domains of matrix metalloprotease-1 (MMP1) on type 1 collagen fibrils correlate with its activity. Using single-molecule Förster resonance energy transfer, we identified functionally relevant open conformations in which the two MMP1 domains are well separated, which were significantly absent for catalytically inactive point mutant (E219Q) of MMP1 and could be modulated by an inhibitor or an enhancer of activity. The observed relevance of open conformations resolves the debate about the roles of open and closed MMP1 structures in function. We fitted the histograms of single-molecule Förster resonance energy transfer values to a sum of two Gaussians and the autocorrelations to an exponential and power law. We used a two-state Poisson process to describe the dynamics and calculate the kinetic rates from the fit parameters. All-atom and coarse-grained simulations reproduced some of the experimental features and revealed substrate-dependent MMP1 dynamics. Our results suggest that an interdomain separation facilitates opening up the catalytic pocket so that the collagen chains come closer to the MMP1 active site. Coordination of functional conformations at different parts of MMP1 occurs via allosteric communications that can take place via interactions mediated by collagen even if the linker between the domains is absent. Modeling dynamics as a Poisson process enables connecting the picosecond timescales of molecular dynamics simulations with the millisecond timescales of single-molecule measurements. Water-soluble MMP1 interacting with water-insoluble collagen fibrils poses challenges for biochemical studies that the single-molecule tracking can overcome for other insoluble substrates. Interdomain communications are likely important for multidomain proteins.
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Affiliation(s)
- Lokender Kumar
- Department of Physics, Colorado School of Mines, Golden, Colorado
| | - Anthony Nash
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Chase Harms
- Department of Physics, Colorado School of Mines, Golden, Colorado
| | - Joan Planas-Iglesias
- Warwick Medical School, University of Warwick, Coventry, United Kingdom; Loschmidt Laboratories, Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Derek Wright
- Department of Physics, Colorado School of Mines, Golden, Colorado
| | - Judith Klein-Seetharaman
- Warwick Medical School, University of Warwick, Coventry, United Kingdom; Department of Chemistry, Colorado School of Mines, Golden, Colorado
| | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, Golden, Colorado.
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11
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Mendoza-Wilson AM, Balandrán-Quintana RR. Computational and Experimental Progress on the Structure and Chemical Reactivity of Procyanidins: Their Potential as Metalloproteinases Inhibitors. CURR ORG CHEM 2019. [DOI: 10.2174/1385272822666180828114021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Matrix metalloproteinases (MMPs) are enzymes involved in various physiological
processes essential for living beings, but the loss of the regulatory control by endogenous
inhibitors of MMPs, leads to the development of serious diseases such as cardiovascular
system affections, cancer, and metastasis. For these reasons, exogenous inhibitors
are required for these enzymes, which are able to control the proteolytic activity
and are selective towards the different MMPs, besides properties which, from the
pharmacological point of view, are necessary to be effective under physiological
conditions. Based on these expectations, some bioactive compounds that are abundant in
the human diet, like procyanidins (PCs) have emerged as potential exogenous inhibitors
of MMPs. This review presents the advances of experimental and computational investigations
carried out to date on the structure and chemical reactivity of PCs, to support the basis of their potential
use as MMP inhibitors. For such purpose, specific sites among MMPs identified for a selective inhibition, the
role of PCs in the regulation of MMPs by posttranscriptional mechanisms at the level of microRNAs, modulation
of reactive oxygen species (ROS), effects on tissue inhibitors of MMPs (TIMPs), the crosslinking of PCs
with the extracellular matrix proteins, as well as direct interaction between PCs and MMPs, are discussed.
Methods for isolation and synthesis of PCs, as well as hydrophilicity properties, bioavailability, and susceptibility
to be metabolized in oral intake, are also addressed. The information gathered in this review could additionally
help to visualize future research related to this topic.
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Affiliation(s)
- Ana María Mendoza-Wilson
- Centro de Investigacion en Alimentacion y Desarrollo, A.C., Coordinacion de Tecnologia de Alimentos de Origen Vegetal, Carretera a La Victoria km 0.6, 83304, Hermosillo, Son, Mexico
| | - René Renato Balandrán-Quintana
- Centro de Investigacion en Alimentacion y Desarrollo, A.C., Coordinacion de Tecnologia de Alimentos de Origen Vegetal, Carretera a La Victoria km 0.6, 83304, Hermosillo, Son, Mexico
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12
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Cerofolini L, Fragai M, Luchinat C. Mechanism and Inhibition of Matrix Metalloproteinases. Curr Med Chem 2019; 26:2609-2633. [PMID: 29589527 DOI: 10.2174/0929867325666180326163523] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 01/02/2023]
Abstract
Matrix metalloproteinases hydrolyze proteins and glycoproteins forming the extracellular matrix, cytokines and growth factors released in the extracellular space, and membrane-bound receptors on the outer cell membrane. The pathological relevance of MMPs has prompted the structural and functional characterization of these enzymes and the development of synthetic inhibitors as possible drug candidates. Recent studies have provided a better understanding of the substrate preference of the different members of the family, and structural data on the mechanism by which these enzymes hydrolyze the substrates. Here, we report the recent advancements in the understanding of the mechanism of collagenolysis and elastolysis, and we discuss the perspectives of new therapeutic strategies for targeting MMPs.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
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13
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Falconer AMD, Chan CM, Gray J, Nagashima I, Holland RA, Shimizu H, Pickford AR, Rowan AD, Wilkinson DJ. Collagenolytic matrix metalloproteinases antagonize proteinase-activated receptor-2 activation, providing insights into extracellular matrix turnover. J Biol Chem 2019; 294:10266-10277. [PMID: 31110047 PMCID: PMC6664178 DOI: 10.1074/jbc.ra119.006974] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/14/2019] [Indexed: 12/11/2022] Open
Abstract
The collagenase subfamily of matrix metalloproteinases (MMPs) have important roles in the remodeling of collagenous matrices. The proteinase-activated receptor (PAR) family has a unique mechanism of activation requiring proteolysis of an extracellular domain forming a neo-N terminus that acts as a tethered ligand, a process that has been associated with the development of arthritis. Canonical PAR2 activation typically occurs via a serine proteinase at Arg36-Ser37, but other proteinases can cleave PARs downstream of the tethered ligand and "disarm" the receptor. To identify additional cleavage sites within PAR2, we synthesized a 42-amino-acid peptide corresponding to the extracellular region. We observed that all three soluble MMP collagenases, MMP-1, MMP-8, and MMP-13, cleave PAR2 and discovered a novel cleavage site (Ser37-Leu38). Metalloproteinases from resorbing bovine nasal cartilage and recombinant human collagenases could cleave a quenched fluorescent peptide mimicking the canonical PAR2 activation region, and kinetic constants were determined. In PAR2-overexpressing SW1353 chondrocytes, we demonstrated that the activator peptide SLIGKV-NH2 induces rapid calcium flux, inflammatory gene expression (including MMP1 and MMP13), and the phosphorylation of extracellular signal-regulated kinase (ERK) and p38 kinase. The corresponding MMP cleavage-derived peptide (LIGKVD-NH2) exhibited no canonical activation; however, we observed phosphorylation of ERK, providing evidence of biased agonism. Importantly, we demonstrated that preincubation with active MMP-1 reduced downstream PAR2 activation by a canonical activator, matriptase, but not SLIGKV-NH2 These results support a role for collagenases as proteinases capable of disarming PAR2, revealing a mechanism that suppresses PAR2-mediated inflammatory responses.
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Affiliation(s)
- Adrian M D Falconer
- From the Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle-upon-Tyne NE1 3BZ, United Kingdom
| | - Chun Ming Chan
- From the Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle-upon-Tyne NE1 3BZ, United Kingdom
| | - Joseph Gray
- Institute of Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Izuru Nagashima
- Bio-material Engineering Research Group, Bioproduction Research Institute, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido 062-8517, Japan, and
| | - Robert A Holland
- Centre for Enzyme Innovation, School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, King Henry Building, King Henry I Street, Portsmouth PO1 2DY, United Kingdom
| | - Hiroki Shimizu
- Bio-material Engineering Research Group, Bioproduction Research Institute, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido 062-8517, Japan, and
| | - Andrew R Pickford
- Centre for Enzyme Innovation, School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, King Henry Building, King Henry I Street, Portsmouth PO1 2DY, United Kingdom
| | - Andrew D Rowan
- From the Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle-upon-Tyne NE1 3BZ, United Kingdom
| | - David J Wilkinson
- From the Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle-upon-Tyne NE1 3BZ, United Kingdom,
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14
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Crucial residues in falcipains that mediate hemoglobin hydrolysis. Exp Parasitol 2019; 197:43-50. [PMID: 30648557 DOI: 10.1016/j.exppara.2019.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/03/2018] [Accepted: 01/11/2019] [Indexed: 02/08/2023]
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15
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Pahwa S, Bhowmick M, Amar S, Cao J, Strongin AY, Fridman R, Weiss SJ, Fields GB. Characterization and regulation of MT1-MMP cell surface-associated activity. Chem Biol Drug Des 2018; 93:1251-1264. [PMID: 30480376 DOI: 10.1111/cbdd.13450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/18/2018] [Accepted: 11/11/2018] [Indexed: 12/19/2022]
Abstract
Quantitative assessment of MT1-MMP cell surface-associated proteolytic activity remains undefined. Presently, MT1-MMP was stably expressed and a cell-based FRET assay developed to quantify activity toward synthetic collagen-model triple-helices. To estimate the importance of cell surface localization and specific structural domains on MT1-MMP proteolysis, activity measurements were performed using a series of membrane-anchored MT1-MMP mutants and compared directly with those of soluble MT1-MMP. MT1-MMP activity (kcat /KM ) on the cell surface was 4.8-fold lower compared with soluble MT1-MMP, with the effect largely manifested in kcat . Deletion of the MT1-MMP cytoplasmic tail enhanced cell surface activity, with both kcat and KM values affected, while deletion of the hemopexin-like domain negatively impacted KM and increased kcat . Overall, cell surface localization of MT1-MMP restricts substrate binding and protein-coupled motions (based on changes in both kcat and KM ) for catalysis. Comparison of soluble and cell surface-bound MT2-MMP revealed 12.9-fold lower activity on the cell surface. The cell-based assay was utilized for small molecule and triple-helical transition state analog MMP inhibitors, which were found to function similarly in solution and at the cell surface. These studies provide the first quantitative assessments of MT1-MMP activity and inhibition in the native cellular environment of the enzyme.
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Affiliation(s)
- Sonia Pahwa
- Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida
| | - Manishabrata Bhowmick
- Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida
| | - Sabrina Amar
- Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida.,Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, Florida
| | - Jian Cao
- Departments of Medicine/Cancer Prevention and Pathology, Stony Brook University, Stony Brook, New York
| | - Alex Y Strongin
- Cancer Research Center, Sanford Burnham Prebys Medical Research Institute, La Jolla, California
| | - Rafael Fridman
- Department of Pathology and the Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Stephen J Weiss
- Division of Molecular Medicine & Genetics, Department of Internal Medicine, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Gregg B Fields
- Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida.,Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, Florida.,The Scripps Research Institute/Scripps Florida, Jupiter, Florida
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16
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Tokmina-Roszyk M, Fields GB. Dissecting MMP P 10' and P 11' subsite sequence preferences, utilizing a positional scanning, combinatorial triple-helical peptide library. J Biol Chem 2018; 293:16661-16676. [PMID: 30185620 DOI: 10.1074/jbc.ra118.003266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/01/2018] [Indexed: 11/06/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases that remodel the extracellular matrix environment and mitigate outside-in signaling. Loss of regulation of MMP activity plays a role in numerous pathological states. In particular, aberrant collagenolysis affects tumor invasion and metastasis, osteoarthritis, and cardiovascular and neurodegenerative diseases. To evaluate the collagen sequence preferences of MMPs, a positional scanning synthetic combinatorial library was synthesized herein and was used to investigate the P10' and P11' substrate subsites. The scaffold for the library was a triple-helical peptide mimic of the MMP cleavage site in types I-III collagen. A FRET-based enzyme activity assay was used to evaluate the sequence preferences of eight MMPs. Deconvolution of the library data revealed distinct motifs for several MMPs and discrimination among closely related MMPs. On the basis of the screening results, several individual peptides were designed and evaluated. A triple-helical substrate incorporating Asp-Lys in the P10'-P11' subsites offered selectivity between MMP-14 and MMP-15, whereas Asp-Lys or Trp-Lys in these subsites discriminated between MMP-2 and MMP-9. Future screening of additional subsite positions will enable the design of selective triple-helical MMP probes that could be used for monitoring in vivo enzyme activity and enzyme-facilitated drug delivery. Furthermore, selective substrates could serve as the basis for the design of specific triple-helical peptide inhibitors targeting only those MMPs that play a detrimental role in a disease of interest.
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Affiliation(s)
- Michal Tokmina-Roszyk
- From the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458 and
| | - Gregg B Fields
- From the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458 and .,the Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, Florida 33458
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17
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Kumar L, Colomb W, Czerski J, Cox CR, Sarkar SK. Efficient protease based purification of recombinant matrix metalloprotease-1 in E. coli. Protein Expr Purif 2018; 148:59-67. [DOI: 10.1016/j.pep.2018.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/24/2018] [Accepted: 04/03/2018] [Indexed: 11/16/2022]
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18
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Gioia M, Fasciglione GF, Sbardella D, Sciandra F, Casella M, Camerini S, Crescenzi M, Gori A, Tarantino U, Cozza P, Brancaccio A, Coletta M, Bozzi M. The enzymatic processing of α-dystroglycan by MMP-2 is controlled by two anchoring sites distinct from the active site. PLoS One 2018; 13:e0192651. [PMID: 29447293 PMCID: PMC5813964 DOI: 10.1371/journal.pone.0192651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/26/2018] [Indexed: 11/19/2022] Open
Abstract
Dystroglycan (DG) is a membrane receptor, belonging to the dystrophin-glycoprotein complex (DGC) and formed by two subunits, α-dystroglycan (α-DG) and β-dystroglycan (β -DG). The C-terminal domain of α-DG and the N-terminal extracellular domain of β -DG are connected, providing a link between the extracellular matrix and the cytosol. Under pathological conditions, such as cancer and muscular dystrophies, DG may be the target of metalloproteinases MMP-2 and MMP-9, contributing to disease progression. Previously, we reported that the C-terminal domain α-DG (483–628) domain is particularly susceptible to the catalytic activity of MMP-2; here we show that the α-DG 621–628 region is required to carry out its complete digestion, suggesting that this portion may represent a MMP-2 anchoring site. Following this observation, we synthesized an α-DG based-peptide, spanning the (613–651) C-terminal region. The analysis of the kinetic and thermodynamic parameters of the whole and the isolated catalytic domain of MMP-2 (cdMMP-2) has shown its inhibitory properties, indicating the presence of (at least) two binding sites for the peptide, both located within the catalytic domain, only one of the two being topologically distinct from the catalytic active groove. However, the different behavior between whole MMP-2 and cdMMP-2 envisages the occurrence of an additional binding site for the peptide on the hemopexin-like domain of MMP-2. Interestingly, mass spectrometry analysis has shown that α-DG (613–651) peptide is cleavable even though it is a very poor substrate of MMP-2, a feature that renders this molecule a promising template for developing a selective MMP-2 inhibitor.
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Affiliation(s)
- Magda Gioia
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- CIRCMSB, Bari, Italy
- * E-mail: (MG); (MB)
| | - Giovanni Francesco Fasciglione
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- CIRCMSB, Bari, Italy
| | - Diego Sbardella
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- CIRCMSB, Bari, Italy
| | | | | | | | | | | | - Umberto Tarantino
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
| | - Paola Cozza
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
| | - Andrea Brancaccio
- CNR Institute for Molecular Recognition, Roma Italy
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
- CIRCMSB, Bari, Italy
| | - Manuela Bozzi
- CNR Institute for Molecular Recognition, Roma Italy
- Institute of Biochemistry and Clinical Biochemistry, Catholic University, Roma Italy
- * E-mail: (MG); (MB)
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19
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Karabencheva-Christova TG, Christov CZ, Fields GB. Conformational Dynamics of Matrix Metalloproteinase-1·Triple-Helical Peptide Complexes. J Phys Chem B 2017; 122:5316-5326. [DOI: 10.1021/acs.jpcb.7b09771] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Tatyana G. Karabencheva-Christova
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Christo Z. Christov
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Gregg B. Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
- Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, Florida 33458, United States
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20
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Radisky ES, Raeeszadeh-Sarmazdeh M, Radisky DC. Therapeutic Potential of Matrix Metalloproteinase Inhibition in Breast Cancer. J Cell Biochem 2017; 118:3531-3548. [PMID: 28585723 PMCID: PMC5621753 DOI: 10.1002/jcb.26185] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 12/14/2022]
Abstract
Matrix metalloproteinases (MMPs) are a family of zinc endopeptidases that cleave nearly all components of the extracellular matrix as well as many other soluble and cell-associated proteins. MMPs have been implicated in normal physiological processes, including development, and in the acquisition and progression of the malignant phenotype. Disappointing results from a series of clinical trials testing small molecule, broad spectrum MMP inhibitors as cancer therapeutics led to a re-evaluation of how MMPs function in the tumor microenvironment, and ongoing research continues to reveal that these proteins play complex roles in cancer development and progression. It is now clear that effective targeting of MMPs for therapeutic benefit will require selective inhibition of specific MMPs. Here, we provide an overview of the MMP family and its biological regulators, the tissue inhibitors of metalloproteinases (TIMPs). We then summarize recent research from model systems that elucidate how specific MMPs drive the malignant phenotype of breast cancer cells, including acquisition of cancer stem cell features and induction of the epithelial-mesenchymal transition, and we also outline clinical studies that implicate specific MMPs in breast cancer outcomes. We conclude by discussing ongoing strategies for development of inhibitors with therapeutic potential that are capable of selectively targeting the MMPs most responsible for tumor promotion, with special consideration of the potential of biologics including antibodies and engineered proteins based on the TIMP scaffold. J. Cell. Biochem. 118: 3531-3548, 2017. © 2017 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville 32224, Florida
| | | | - Derek C Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville 32224, Florida
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21
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Using Small Angle X-Ray Scattering (SAXS) to Characterize the Solution Conformation and Flexibility of Matrix Metalloproteinases (MMPs). Methods Mol Biol 2017. [PMID: 28299734 DOI: 10.1007/978-1-4939-6863-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Small angle X-ray scattering (SAXS) provides information about the conformation and flexibility of proteins in solution, and hence provides complementary structural information to that obtained from X-ray crystallography and nuclear magnetic resonance spectroscopy. In this chapter, we describe the methods for the preparation of matrix metalloproteinase (MMP) samples for SAXS analyses, and for the acquisition, processing and interpretation of the SAXS data.
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22
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Karabencheva-Christova TG, Christov CZ, Fields GB. Collagenolytic Matrix Metalloproteinase Structure–Function Relationships: Insights From Molecular Dynamics Studies. STRUCTURAL AND MECHANISTIC ENZYMOLOGY 2017; 109:1-24. [DOI: 10.1016/bs.apcsb.2017.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Greene T, Lin TY, Andrisani OM, Lin CC. Comparative study of visible light polymerized gelatin hydrogels for 3D culture of hepatic progenitor cells. J Appl Polym Sci 2016. [DOI: 10.1002/app.44585] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Tanja Greene
- Department of Biomedical Engineering; Indiana University-Purdue University Indianapolis; Indianapolis Indiana 46202
| | - Tsai-Yu Lin
- Department of Biomedical Engineering; Indiana University-Purdue University Indianapolis; Indianapolis Indiana 46202
| | - Ourania M. Andrisani
- Department of Basic Medical Sciences and Purdue Center for Cancer Research; Purdue University; West Lafayette Indiana 47907
| | - Chien-Chi Lin
- Department of Biomedical Engineering; Indiana University-Purdue University Indianapolis; Indianapolis Indiana 46202
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24
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Singh W, Fields GB, Christov CZ, Karabencheva-Christova TG. Effects of Mutations on Structure-Function Relationships of Matrix Metalloproteinase-1. Int J Mol Sci 2016; 17:ijms17101727. [PMID: 27754420 PMCID: PMC5085758 DOI: 10.3390/ijms17101727] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 09/16/2016] [Accepted: 10/03/2016] [Indexed: 02/06/2023] Open
Abstract
Matrix metalloproteinase-1 (MMP-1) is one of the most widely studied enzymes involved in collagen degradation. Mutations of specific residues in the MMP-1 hemopexin-like (HPX) domain have been shown to modulate activity of the MMP-1 catalytic (CAT) domain. In order to reveal the structural and conformational effects of such mutations, a molecular dynamics (MD) study was performed of in silico mutated residues in the X-ray crystallographic structure of MMP-1 complexed with a collagen-model triple-helical peptide (THP). The results indicate an important role of the mutated residues in MMP-1 interactions with the THP and communication between the CAT and the HPX domains. Each mutation has a distinct impact on the correlated motions in the MMP-1•THP. An increased collagenase activity corresponded to the appearance of a unique anti-correlated motion and decreased correlated motions, while decreased collagenase activity corresponded both to increased and decreased anti-correlated motions.
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Affiliation(s)
- Warispreet Singh
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.
| | - Gregg B Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL 33458, USA.
- Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, FL 33458, USA.
| | - Christo Z Christov
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.
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25
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Subramanian SR, Singam ERA, Berinski M, Subramanian V, Wade RC. Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen. J Phys Chem B 2016; 120:8580-9. [PMID: 27245212 DOI: 10.1021/acs.jpcb.6b02573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sequence-specific cleavage of collagen by mammalian collagenase plays a pivotal role in cell function. Collagenases are matrix metalloproteinases that cleave the peptide bond at a specific position on fibrillar collagen. The collagenase Hemopexin-like (HPX) domain has been proposed to be responsible for substrate recognition, but the mechanism by which collagenases identify the cleavage site on fibrillar collagen is not clearly understood. In this study, Brownian dynamics simulations coupled with atomic-detail and coarse-grained molecular dynamics simulations were performed to dock matrix metalloproteinase-1 (MMP-1) on a collagen IIIα1 triple helical peptide. We find that the HPX domain recognizes the collagen triple helix at a conserved R-X11-R motif C-terminal to the cleavage site to which the HPX domain of collagen is guided electrostatically. The binding of the HPX domain between the two arginine residues is energetically stabilized by hydrophobic contacts with collagen. From the simulations and analysis of the sequences and structural flexibility of collagen and collagenase, a mechanistic scheme by which MMP-1 can recognize and bind collagen for proteolysis is proposed.
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Affiliation(s)
- Sundar Raman Subramanian
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35, 69117 Heidelberg, Germany.,Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Chennai, India
| | - Ettayapuram Ramaprasad Azhagiya Singam
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35, 69117 Heidelberg, Germany.,Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Chennai, India
| | - Michael Berinski
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35, 69117 Heidelberg, Germany.,Edinburgh Genomics, The University of Edinburgh , Edinburgh, Scotland
| | - Venkatesan Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Chennai, India
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35, 69117 Heidelberg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg , Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University , Heidelberg, Germany
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26
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Azhagiya Singam ER, Rajapandian V, Subramanian V. Molecular dynamics simulation study on the interaction of collagen-like peptides with gelatinase-A (MMP-2). Biopolymers 2016; 101:779-94. [PMID: 24374600 DOI: 10.1002/bip.22457] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 12/21/2013] [Accepted: 12/21/2013] [Indexed: 12/19/2022]
Abstract
Although several models have been proposed for the interaction of collagen with gelatinase-A (matrix metalloproteinases-2 (MMP-2)), the extensive role of each domain of gelatinase A in hydrolyzing the collagens with and without interruptions is still elusive. Molecular docking, molecular dynamics (MD) simulation, normal mode analysis (NMA) and framework rigidity optimized dynamics algorithm (FRODAN) based analysis were carried out to understand the function of various domains of MMP-2 upon interaction with collagen like peptides. The results reveal that the collagen binding domain (CBD) binds to the C-terminal of collagen like peptide with interruption. CBD helps in unwinding the loosely packed interrupted region of triple helical structure to a greater extent. It can be possible to speculate that the role of hemopexin (HPX) domain is to prevent further unwinding of collagen like peptide by binding to the other end of the collagen like peptide. The catalytic (CAT) domain then reorients itself to interact with the part of the unwound region of collagen like peptide for further hydrolysis. In conclusion the CBD of MMP-2 recognizes the collagen and aids in unwinding the collagen like peptide with interruptions, and the HPX domain of MMP-2 binds to the other end of the collagen allowing CAT domain to access the cleavage site. This study provides a comprehensive understanding of the structural basis of collagenolysis by MMP-2.
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Affiliation(s)
- E R Azhagiya Singam
- Chemical Laboratory, Council of Scientific and Industrial Research, Central Leather Research Institute, Adyar, Chennai, 600 020, Tamil Nadu, India
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27
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Singh W, Fields GB, Christov CZ, Karabencheva-Christova TG. Importance of the Linker Region in Matrix Metalloproteinase-1 Domain Interactions. RSC Adv 2016; 6:23223-23232. [PMID: 26998255 DOI: 10.1039/c6ra03033e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Collagenolysis is catalyzed by enzymes from the matrix metalloproteinase (MMP) family, where one of the most studied is MMP-1. The X-ray crystallographic structure of MMP-1 complexed with a collagen-model triple-helical peptide (THP) provided important atomistic information, but few details on the effects of the conformational flexibility on catalysis. In addition, the role of the linker region between the catalytic (CAT) and hemopexin-like (HPX) domains was not defined. In order to reveal the dynamics and correlations of MMP-1 comprehensive atomistic molecular dynamics simulations of an MMP-1•THP complex was performed. To examine the role of the linker region for MMP-1 function simulations with linker regions from MT1-MMP/MMP-14 and MMP-13 replacing the MMP-1 linker region were performed. The MD studies were in good agreement with the experimental observation that in the MMP-1•THP X-ray crystallographic structure MMP-1 is in a "closed" conformation. MD revealed that the interactions of the THP with the both the CAT and HPX domains of MMP-1 are dynamic in nature, and the linker region of MMP-1 influences the interactions and dynamics of both the CAT and HPX domains and collagen binding to MMP-1.
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Affiliation(s)
- Warispreet Singh
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - Gregg B Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, FL 33458, USA; Department of Chemistry, The Scripps Research Institute/Scripps Florida, Jupiter, FL 33458, USA
| | - Christo Z Christov
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
| | - Tatyana G Karabencheva-Christova
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, United Kingdom
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28
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Prior SH, Byrne TS, Tokmina-Roszyk D, Fields GB, Van Doren SR. Path to Collagenolysis: COLLAGEN V TRIPLE-HELIX MODEL BOUND PRODUCTIVELY AND IN ENCOUNTERS BY MATRIX METALLOPROTEINASE-12. J Biol Chem 2016; 291:7888-901. [PMID: 26887942 DOI: 10.1074/jbc.m115.703124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 11/06/2022] Open
Abstract
Collagenolysis is essential in extracellular matrix homeostasis, but its structural basis has long been shrouded in mystery. We have developed a novel docking strategy guided by paramagnetic NMR that positions a triple-helical collagen V mimic (synthesized with nitroxide spin labels) in the active site of the catalytic domain of matrix metalloproteinase-12 (MMP-12 or macrophage metalloelastase) primed for catalysis. The collagenolytically productive complex forms by utilizing seven distinct subsites that traverse the entire length of the active site. These subsites bury ∼1,080 Å(2)of surface area, over half of which is contributed by the trailing strand of the synthetic collagen V mimic, which also appears to ligate the catalytic zinc through the glycine carbonyl oxygen of its scissile G∼VV triplet. Notably, the middle strand also occupies the full length of the active site where it contributes extensive interfacial contacts with five subsites. This work identifies, for the first time, the productive and specific interactions of a collagen triple helix with an MMP catalytic site. The results uniquely demonstrate that the active site of the MMPs is wide enough to accommodate two strands from collagen triple helices. Paramagnetic relaxation enhancements also reveal an extensive array of encounter complexes that form over a large part of the catalytic domain. These transient complexes could possibly facilitate the formation of collagenolytically active complexes via directional Brownian tumbling.
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Affiliation(s)
- Stephen H Prior
- From the Department of Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Todd S Byrne
- From the Department of Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Dorota Tokmina-Roszyk
- the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, and
| | - Gregg B Fields
- the Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, and the Scripps Research Institute/Scripps Florida, Jupiter, Florida 33458
| | - Steven R Van Doren
- From the Department of Biochemistry, University of Missouri, Columbia, Missouri 65211,
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29
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Abstract
Using NMR spectroscopy, Zhao and colleagues, in this issue, have modeled the short-lived complex formed between the MT1-MMP hemopexin domain and a synthetic triple-helical collagen mimetic. Their model is consistent with two alternative mechanisms for the breakdown of collagen by the enzyme.
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30
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Zhao Y, Marcink TC, Sanganna Gari RR, Marsh BP, King GM, Stawikowska R, Fields GB, Van Doren SR. Transient collagen triple helix binding to a key metalloproteinase in invasion and development. Structure 2015; 23:257-69. [PMID: 25651059 DOI: 10.1016/j.str.2014.11.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/30/2014] [Accepted: 11/17/2014] [Indexed: 12/17/2022]
Abstract
Skeletal development and invasion by tumor cells depends on proteolysis of collagen by the pericellular metalloproteinase MT1-MMP. Its hemopexin-like (HPX) domain binds to collagen substrates to facilitate their digestion. Spin labeling and paramagnetic nuclear magnetic resonance (NMR) detection have revealed how the HPX domain docks to collagen I-derived triple helix. Mutations impairing triple-helical peptidase activity corroborate the interface. Saturation transfer difference NMR suggests rotational averaging around the longitudinal axis of the triple-helical peptide. Part of the interface emerges as unique and potentially targetable for selective inhibition. The triple helix crosses the junction of blades I and II at a 45° angle to the symmetry axis of the HPX domain, placing the scissile Gly∼Ile bond near the HPX domain and shifted ∼25 Å from MMP-1 complexes. This raises the question of the MT1-MMP catalytic domain folding over the triple helix during catalysis, a possibility accommodated by the flexibility between domains suggested by atomic force microscopy images.
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Affiliation(s)
- Yingchu Zhao
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA
| | - Thomas C Marcink
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA
| | | | - Brendan P Marsh
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
| | - Gavin M King
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA; Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
| | - Roma Stawikowska
- Torrey Pines Institute for Molecular Studies, 11350 Southwest Village Parkway, Port Saint Lucie, FL 34987, USA
| | - Gregg B Fields
- Torrey Pines Institute for Molecular Studies, 11350 Southwest Village Parkway, Port Saint Lucie, FL 34987, USA
| | - Steven R Van Doren
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA.
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31
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Radisky ES, Radisky DC. Matrix metalloproteinases as breast cancer drivers and therapeutic targets. Front Biosci (Landmark Ed) 2015; 20:1144-63. [PMID: 25961550 DOI: 10.2741/4364] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Members of the matrix metalloproteinase (MMP) family have been identified as poor prognosis markers for breast cancer patients and as drivers of many facets of the tumor phenotype in experimental models. Early enthusiasm for MMPs as therapeutic targets was tempered following disappointing clinical trials that utilized broad spectrum, small molecule catalytic site inhibitors. However, subsequent research has continued to define key roles for MMPs as breast cancer promoters, to elucidate the complex roles that that these proteins play in breast cancer development and progression, and to identify how these roles are linked to specific and unique biochemical features of individual members of the MMP family. Here, we provide an overview of the structural features of the MMPs, then discuss clinical studies identifying which MMP family members are linked with breast cancer development and new experimental studies that reveal how these specific MMPs may play unique roles in the breast cancer microenvironment. We conclude with a discussion of the most promising avenues for development of therapeutic agents capable of targeting the tumor-promoting properties of MMPs.
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Affiliation(s)
- Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224,
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32
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Matrix metalloproteinase interactions with collagen and elastin. Matrix Biol 2015; 44-46:224-31. [PMID: 25599938 PMCID: PMC4466143 DOI: 10.1016/j.matbio.2015.01.005] [Citation(s) in RCA: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/10/2015] [Accepted: 01/10/2015] [Indexed: 12/18/2022]
Abstract
Most abundant in the extracellular matrix are collagens, joined by elastin that confers elastic recoil to the lung, aorta, and skin. These fibrils are highly resistant to proteolysis but can succumb to a minority of the matrix metalloproteinases (MMPs). Considerable inroads to understanding how such MMPs move to the susceptible sites in collagen and then unwind the triple helix of collagen monomers have been gained. The essential role in unwinding of the hemopexin-like domain of interstitial collagenases or the collagen binding domain of gelatinases is highlighted. Elastolysis is also facilitated by the collagen binding domain in the cases of MMP-2 and MMP-9, and remote exosites of the catalytic domain in the case of MMP-12.
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33
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Grasso G. Monitoring the biomolecular interactions and the activity of Zn-containing enzymes involved in conformational diseases: experimental methods for therapeutic purposes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 97:115-42. [PMID: 25458357 DOI: 10.1016/bs.apcsb.2014.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Zinc metalloproteases (ZnMPs) participate in diverse biological reactions, encompassing the synthesis and degradation of all the major metabolites in living organisms. In particular, ZnMPs have been recognized to play a very important role in controlling the concentration level of several peptides and/or proteins whose homeostasis has to be finely regulated for the correct physiology of cells. Dyshomeostasis of aggregation-prone proteins causes pathological conditions and the development of several different diseases. For this reason, in recent years, many analytical approaches have been applied for studying the interaction between ZnMPs and their substrates/inhibitors and how environmental factors can affect enzyme activities. In this scenario, nuclear magnetic resonance, X-ray diffraction, mass spectrometric (MS), and optical methods occupy a very important role in elucidating different aspects of the ZnMPs-substrates/inhibitors interaction, ranging from identification of cleavage sites to quantitation of kinetic parameters and inhibition constants. Here, an overview of all the main achievements in the application of different experimental approaches with special attention to MS methods to the investigation of ZnMPs-substrates/inhibitors interaction is given. A general MS experimental protocol which has been proved to be useful to study such interactions is also described.
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Affiliation(s)
- Giuseppe Grasso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy.
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34
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Basis for substrate recognition and distinction by matrix metalloproteinases. Proc Natl Acad Sci U S A 2014; 111:E4148-55. [PMID: 25246591 DOI: 10.1073/pnas.1406134111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Genomic sequencing and structural genomics produced a vast amount of sequence and structural data, creating an opportunity for structure-function analysis in silico [Radivojac P, et al. (2013) Nat Methods 10(3):221-227]. Unfortunately, only a few large experimental datasets exist to serve as benchmarks for function-related predictions. Furthermore, currently there are no reliable means to predict the extent of functional similarity among proteins. Here, we quantify structure-function relationships among three phylogenetic branches of the matrix metalloproteinase (MMP) family by comparing their cleavage efficiencies toward an extended set of phage peptide substrates that were selected from ∼ 64 million peptide sequences (i.e., a large unbiased representation of substrate space). The observed second-order rate constants [k(obs)] across the substrate space provide a distance measure of functional similarity among the MMPs. These functional distances directly correlate with MMP phylogenetic distance. There is also a remarkable and near-perfect correlation between the MMP substrate preference and sequence identity of 50-57 discontinuous residues surrounding the catalytic groove. We conclude that these residues represent the specificity-determining positions (SDPs) that allowed for the expansion of MMP proteolytic function during evolution. A transmutation of only a few selected SDPs proximal to the bound substrate peptide, and contributing the most to selectivity among the MMPs, is sufficient to enact a global change in the substrate preference of one MMP to that of another, indicating the potential for the rational and focused redesign of cleavage specificity in MMPs.
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35
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Bastos IMD, Motta FN, Grellier P, Santana JM. Parasite prolyl oligopeptidases and the challenge of designing chemotherapeuticals for Chagas disease, leishmaniasis and African trypanosomiasis. Curr Med Chem 2014; 20:3103-15. [PMID: 23514419 PMCID: PMC3778648 DOI: 10.2174/0929867311320250006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/16/2012] [Indexed: 11/22/2022]
Abstract
The trypanosomatids Trypanosoma cruzi, Leishmania spp. and Trypanosoma brucei spp. cause Chagas disease, leishmaniasis and human African trypanosomiasis, respectively. It is estimated that over 10 million people worldwide suffer from these neglected diseases, posing enormous social and economic problems in endemic areas. There are no vaccines to prevent these infections and chemotherapies are not adequate. This picture indicates that new chemotherapeutic agents must be developed to treat these illnesses. For this purpose, understanding the biology of the pathogenic trypanosomatid-host cell interface is fundamental for molecular and functional characterization of virulence factors that may be used as targets for the development of inhibitors to be used for effective chemotherapy. In this context, it is well known that proteases have crucial functions for both metabolism and infectivity of pathogens and are thus potential drug targets. In this regard, prolyl oligopeptidase and oligopeptidase B, both members of the S9 serine protease family, have been shown to play important roles in the interactions of pathogenic protozoa with their mammalian hosts and may thus be considered targets for drug design. This review aims to discuss structural and functional properties of these intriguing enzymes and their potential as targets for the development of drugs against Chagas disease, leishmaniasis and African trypanosomiasis.
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Affiliation(s)
- I M D Bastos
- Pathogen-Host Interface Laboratory, Department of Cell Biology, The University of Brasília, Brasília, Brazil
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36
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Lauer JL, Bhowmick M, Tokmina-Roszyk D, Lin Y, Van Doren SR, Fields GB. The role of collagen charge clusters in the modulation of matrix metalloproteinase activity. J Biol Chem 2014; 289:1981-92. [PMID: 24297171 PMCID: PMC3900948 DOI: 10.1074/jbc.m113.513408] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 11/28/2013] [Indexed: 12/22/2022] Open
Abstract
Members of the matrix metalloproteinase (MMP) family selectively cleave collagens in vivo. Several substrate structural features that direct MMP collagenolysis have been identified. The present study evaluated the role of charged residue clusters in the regulation of MMP collagenolysis. A series of 10 triple-helical peptide (THP) substrates were constructed in which either Lys-Gly-Asp or Gly-Asp-Lys motifs replaced Gly-Pro-Hyp (where Hyp is 4-hydroxy-L-proline) repeats. The stabilities of THPs containing the two different motifs were analyzed, and kinetic parameters for substrate hydrolysis by six MMPs were determined. A general trend for virtually all enzymes was that, as Gly-Asp-Lys motifs were moved from the extreme N and C termini to the interior next to the cleavage site sequence, kcat/Km values increased. Additionally, all Gly-Asp-Lys THPs were as good or better substrates than the parent THP in which Gly-Asp-Lys was not present. In turn, the Lys-Gly-Asp THPs were also always better substrates than the parent THP, but the magnitude of the difference was considerably less compared with the Gly-Asp-Lys series. Of the MMPs tested, MMP-2 and MMP-9 most greatly favored the presence of charged residues with preference for the Gly-Asp-Lys series. Lys-Gly-(Asp/Glu) motifs are more commonly found near potential MMP cleavage sites than Gly-(Asp/Glu)-Lys motifs. As Lys-Gly-Asp is not as favored by MMPs as Gly-Asp-Lys, the Lys-Gly-Asp motif appears advantageous over the Gly-Asp-Lys motif by preventing unwanted MMP hydrolysis. More specifically, the lack of Gly-Asp-Lys clusters may diminish potential MMP-2 and MMP-9 collagenolytic activity. The present study indicates that MMPs have interactions spanning the P23-P23' subsites of collagenous substrates.
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Affiliation(s)
- Janelle L. Lauer
- From the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Manishabrata Bhowmick
- From the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987 and
| | - Dorota Tokmina-Roszyk
- From the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987 and
| | - Yan Lin
- From the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Steven R. Van Doren
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211
| | - Gregg B. Fields
- From the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987 and
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37
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Fields GB. Biophysical studies of matrix metalloproteinase/triple-helix complexes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 97:37-48. [PMID: 25458354 PMCID: PMC4337812 DOI: 10.1016/bs.apcsb.2014.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. The structures of MMPs, in solution and solid state and in the presence and absence of triple-helical collagen models, have been assessed by NMR spectroscopy, small-angle X-ray scattering, and X-ray crystallography. Structures observed in solution exhibit flexibility between the MMP catalytic (CAT) and hemopexin-like (HPX) domains, while solid-state structures are relatively compact. Evaluation of the maximum occurrence (MO) of MMP-1 conformations in solution found that, for all the high MO conformations, the CAT and HPX domains are not in tight contact, and the residues of the HPX domain reported to be responsible for the binding to the collagen triple-helix are solvent exposed. A mechanism for collagenolysis has been developed based on analysis of MMP solution structures. Information obtained from solid-state structures has proven valuable for analyzing specific contacts between MMPs and the collagen triple-helix.
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38
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Fragai M, Luchinat C, Parigi G, Ravera E. Conformational freedom of metalloproteins revealed by paramagnetism-assisted NMR. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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Cerofolini L, Fields GB, Fragai M, Geraldes CFGC, Luchinat C, Parigi G, Ravera E, Svergun DI, Teixeira JMC. Examination of matrix metalloproteinase-1 in solution: a preference for the pre-collagenolysis state. J Biol Chem 2013; 288:30659-30671. [PMID: 24025334 DOI: 10.1074/jbc.m113.477240] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Catalysis of collagen degradation by matrix metalloproteinase 1 (MMP-1) has been proposed to critically rely on flexibility between the catalytic (CAT) and hemopexin-like (HPX) domains. A rigorous assessment of the most readily accessed conformations in solution is required to explain the onset of substrate recognition and collagenolysis. The present study utilized paramagnetic NMR spectroscopy and small angle x-ray scattering (SAXS) to calculate the maximum occurrence (MO) of MMP-1 conformations. The MMP-1 conformations with large MO values (up to 47%) are restricted into a relatively small conformational region. All conformations with high MO values differ largely from the closed MMP-1 structures obtained by x-ray crystallography. The MO of the latter is ~20%, which represents the upper limit for the presence of this conformation in the ensemble sampled by the protein in solution. In all the high MO conformations, the CAT and HPX domains are not in tight contact, and the residues of the HPX domain reported to be responsible for the binding to the collagen triple-helix are solvent exposed. Thus, overall analysis of the highest MO conformations indicated that MMP-1 in solution was poised to interact with collagen and then could readily proceed along the steps of collagenolysis.
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Affiliation(s)
| | - Gregg B Fields
- the Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987,.
| | - Marco Fragai
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Carlos F G C Geraldes
- the Center for Neuroscience and Cell Biology and; the Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, P.O. Box 3046, 3001-401 Coimbra, Portugal, and
| | - Claudio Luchinat
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy,.
| | - Giacomo Parigi
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- From the CERM and; the Department of Chemistry "U. Schiff," University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Dmitri I Svergun
- the EMBL, c/o DESY, Notkestrasse 85, Geb. 25 A, 22603 Hamburg, Germany
| | - João M C Teixeira
- From the CERM and; the Center for Neuroscience and Cell Biology and; the Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, P.O. Box 3046, 3001-401 Coimbra, Portugal, and
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40
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Abstract
Interstitial collagen mechanical and biological properties are altered by proteases that catalyze the hydrolysis of the collagen triple-helical structure. Collagenolysis is critical in development and homeostasis but also contributes to numerous pathologies. Mammalian collagenolytic enzymes include matrix metalloproteinases, cathepsin K, and neutrophil elastase, and a variety of invertebrates and pathogens possess collagenolytic enzymes. Components of the mechanism of action for the collagenolytic enzyme MMP-1 have been defined experimentally, and insights into other collagenolytic mechanisms have been provided. Ancillary biomolecules may modulate the action of collagenolytic enzymes.
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Affiliation(s)
- Gregg B Fields
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL 34987, USA.
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41
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Mikhailova M, Xu X, Robichaud TK, Pal S, Fields GB, Steffensen B. Identification of collagen binding domain residues that govern catalytic activities of matrix metalloproteinase-2 (MMP-2). Matrix Biol 2012; 31:380-8. [PMID: 23085623 DOI: 10.1016/j.matbio.2012.10.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 10/10/2012] [Accepted: 10/11/2012] [Indexed: 01/28/2023]
Abstract
An innovative approach to enhance the selectivity of matrix metalloproteinase (MMP) inhibitors comprises targeting these inhibitors to catalytically required substrate binding sites (exosites) that are located outside the catalytic cleft. In MMP-2, positioning of collagen substrate molecules occurs via a unique fibronectin-like domain (CBD) that contains three distinct modular collagen binding sites. To characterize the contributions of these exosites to gelatinolysis by MMP-2, seven MMP-2 variants were generated with single, or concurrent double and triple alanine substitutions in the three fibronectin type II modules of the CBD. Circular dichroism spectroscopy verified that recombinant MMP-2 wild-type (WT) and variants had the same fold. Moreover, the MMP-2 WT and variants had the same activity on a short FRET peptide substrate that is hydrolyzed independently of CBD binding. Among single-point variants, substitution in the module 3 binding site had greatest impact on the affinity of MMP-2 for gelatin. Simultaneous substitutions in two or three CBD modules further reduced gelatin binding. The rates of gelatinolysis of MMP-2 variants were reduced by 20-40% following single-point substitutions, by 60-75% after double-point modifications, and by >90% for triple-point variants. Intriguingly, the three CBD modules contributed differentially to cleavage of dissociated α-1(I) and α-2(I) collagen chains. Importantly, kinetic analyses (k(cat)/K(m)) revealed that catalysis of a triple-helical FRET peptide substrate by MMP-2 relied primarily on the module 3 binding site. Thus, we have identified three collagen binding site residues that are essential for gelatinolysis and constitute promising targets for selective inhibition of MMP-2.
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Affiliation(s)
- Margarita Mikhailova
- Department of Periodontics, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, MC 7894, San Antonio, TX 78229-3900, USA
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42
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Structural insights into triple-helical collagen cleavage by matrix metalloproteinase 1. Proc Natl Acad Sci U S A 2012; 109:12461-6. [PMID: 22761315 DOI: 10.1073/pnas.1204991109] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Collagenases of the matrix metalloproteinase (MMP) family play major roles in morphogenesis, tissue repair, and human diseases, but how they recognize and cleave the collagen triple helix is not fully understood. Here, we report temperature-dependent binding of a catalytically inactive MMP-1 mutant (E200A) to collagen through the cooperative action of its catalytic and hemopexin domains. Contact between the two molecules was mapped by screening the Collagen Toolkit peptide library and by hydrogen/deuterium exchange. The crystal structure of MMP-1(E200A) bound to a triple-helical collagen peptide revealed extensive interactions of the 115-Å-long triple helix with both MMP-1 domains. An exosite in the hemopexin domain, which binds the leucine 10 residues C-terminal to the scissile bond, is critical for collagenolysis and represents a unique target for inhibitor development. The scissile bond is not correctly positioned for hydrolysis in the crystallized complex. A productive binding mode is readily modeled, without altering the MMP-1 structure or the exosite interactions, by axial rotation of the collagen homotrimer. Interdomain flexing of the enzyme and a localized excursion of the collagen chain closest to the active site, facilitated by thermal loosening of the substrate, may lead to the first transition state of collagenolysis.
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43
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Bertini I, Fragai M, Luchinat C, Melikian M, Toccafondi M, Lauer JL, Fields GB. Structural basis for matrix metalloproteinase 1-catalyzed collagenolysis. J Am Chem Soc 2012; 134:2100-10. [PMID: 22239621 PMCID: PMC3298817 DOI: 10.1021/ja208338j] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The proteolysis of collagen triple-helical structure (collagenolysis) is a poorly understood yet critical physiological process. Presently, matrix metalloproteinase 1 (MMP-1) and collagen triple-helical peptide models have been utilized to characterize the events and calculate the energetics of collagenolysis via NMR spectroscopic analysis of 12 enzyme-substrate complexes. The triple-helix is bound initially by the MMP-1 hemopexin-like (HPX) domain via a four amino acid stretch (analogous to type I collagen residues 782-785). The triple-helix is then presented to the MMP-1 catalytic (CAT) domain in a distinct orientation. The HPX and CAT domains are rotated with respect to one another compared with the X-ray "closed" conformation of MMP-1. Back-rotation of the CAT and HPX domains to the X-ray closed conformation releases one chain out of the triple-helix, and this chain is properly positioned in the CAT domain active site for subsequent hydrolysis. The aforementioned steps provide a detailed, experimentally derived, and energetically favorable collagenolytic mechanism, as well as significant insight into the roles of distinct domains in extracellular protease function.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Shiff”, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Shiff”, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Shiff”, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Maxime Melikian
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Mirco Toccafondi
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Janelle L. Lauer
- Department of Biochemistry, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
- Department of Molecular Therapeutics, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Gregg B. Fields
- Department of Biochemistry, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port St. Lucie, FL 34987 USA
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