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Radzki D, Negri A, Kusiak A, Obuchowski M. Matrix Metalloproteinases in the Periodontium-Vital in Tissue Turnover and Unfortunate in Periodontitis. Int J Mol Sci 2024; 25:2763. [PMID: 38474009 DOI: 10.3390/ijms25052763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The extracellular matrix (ECM) is a complex non-cellular three-dimensional macromolecular network present within all tissues and organs, forming the foundation on which cells sit, and composed of proteins (such as collagen), glycosaminoglycans, proteoglycans, minerals, and water. The ECM provides a fundamental framework for the cellular constituents of tissue and biochemical support to surrounding cells. The ECM is a highly dynamic structure that is constantly being remodeled. Matrix metalloproteinases (MMPs) are among the most important proteolytic enzymes of the ECM and are capable of degrading all ECM molecules. MMPs play a relevant role in physiological as well as pathological processes; MMPs participate in embryogenesis, morphogenesis, wound healing, and tissue remodeling, and therefore, their impaired activity may result in several problems. MMP activity is also associated with chronic inflammation, tissue breakdown, fibrosis, and cancer invasion and metastasis. The periodontium is a unique anatomical site, composed of a variety of connective tissues, created by the ECM. During periodontitis, a chronic inflammation affecting the periodontium, increased presence and activity of MMPs is observed, resulting in irreversible losses of periodontal tissues. MMP expression and activity may be controlled in various ways, one of which is the inhibition of their activity by an endogenous group of tissue inhibitors of metalloproteinases (TIMPs), as well as reversion-inducing cysteine-rich protein with Kazal motifs (RECK).
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Affiliation(s)
- Dominik Radzki
- Department of Periodontology and Oral Mucosa Diseases, Faculty of Medicine, Medical University of Gdańsk, 80-208 Gdańsk, Poland
- Division of Molecular Bacteriology, Institute of Medical Biotechnology and Experimental Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, 80-211 Gdańsk, Poland
| | - Alessandro Negri
- Division of Molecular Bacteriology, Institute of Medical Biotechnology and Experimental Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, 80-211 Gdańsk, Poland
| | - Aida Kusiak
- Department of Periodontology and Oral Mucosa Diseases, Faculty of Medicine, Medical University of Gdańsk, 80-208 Gdańsk, Poland
| | - Michał Obuchowski
- Division of Molecular Bacteriology, Institute of Medical Biotechnology and Experimental Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, 80-211 Gdańsk, Poland
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Wiśniowski T, Bryda J, Wątroba S. The role of matrix metalloproteinases in pathogenesis, diagnostics, and treatment of human prostate cancer. POSTEP HIG MED DOSW 2023. [DOI: 10.2478/ahem-2023-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
Abstract
The prostate gland is highly susceptible to oncogenic transformation, many times more than other sex tissues, such as seminal vesicles. In fact, prostate cancer (PCa) will be diagnosed in one in seven lifetime patients, making PCa the subject of intense research aimed at clarifying its biology and providing adequate treatment. PCa is the fourth most common cancer in the world in terms of the overall population and the second most common cancer for the male population. It is postulated that the development of PCa may be influenced by dietary factors, physical and sexual activity, androgens, obesity, and inflammation, but their role in the development of prostate cancer still remains unclear. Extracellular matrix metalloproteinases (MMPs) and tissue metalloproteinase inhibitors (TIMPs) play an important role in many physiological and pathological processes, including proliferation, migration, invasion, cell differentiation, participation in inflammatory processes and angiogenesis. Numerous studies point to a direct relationship between MMPs and both local tumor invasion and the formation of distant metastases. High activity of MMPs is observed in solid tumors of various origins, which positively correlates with a poor overall survival rate. Although biochemical diagnostic markers of PCa are currently available, from the point of view of clinical practice, it seems particularly important to develop new and more sensitive markers allowing for early diagnosis and long-term monitoring of patients after PCa treatment, and the assessment of MMP activity in urine and serum of patients are potential factors that could play such a role.
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Wątroba S, Wiśniowski T, Bryda J, Kurzepa J. Characteristics of matrix metalloproteinases and their role in embryogenesis of the mammalian respiratory system. POSTEP HIG MED DOSW 2021. [DOI: 10.5604/01.3001.0014.6933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Summary
The human respiratory system appears as an outgrowth from the ventral wall of the primary foregut and its development includes a series of subsequent processes, dependent on the interactions between endothelial cells, respiratory epithelium and extracellular matrix (ECM). These interactions determine the acquisition of normal structural and functional features of the newly created tissues. The essential role in the morphogenesis of the respiratory system is performed by matrix metalloproteinases (MMPs). MMPs are endopeptidases containing zinc ion in their active center, necessary for the processes of hydrolysis of peptide bonds of substrates. The production of MMPs takes place in most connective tissue cells, leukocytes, macrophages, vascular endothelial cells as well as in neurons, glial cells and in tumor cells. Like other proteolytic enzymes, MMPs are produced and secreted in the form of inactive pro-enzymes, and their activation occurs in the extracellular space. MMPs perform both physiological and pathological functions during tissue modeling and their role in embryogenesis is based on the regulation of angiogenesis processes, stroma formation and cells migration. This article aims to characterize, discuss and demonstrate the activity and the role of MMPs in the subsequent stages of respiratory development.
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Affiliation(s)
- Sławomir Wątroba
- Department of Neonatology and Neonatal Intensive Care Unit , Independent Public Healthcare , Puławy , Poland
| | - Tomasz Wiśniowski
- Department of Urology and Urological Oncology , St. John of God Independent Public Provincial Hospital , Lublin , Poland
| | - Jarosław Bryda
- Department of Veterinary Hygiene , Voivodship Veterinary Inspectorate , Lublin , Poland
| | - Jacek Kurzepa
- Department of Medical Chemistry , Medical University , Lublin , Poland
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Decaneto E, Vasilevskaya T, Kutin Y, Ogata H, Grossman M, Sagi I, Havenith M, Lubitz W, Thiel W, Cox N. Solvent water interactions within the active site of the membrane type I matrix metalloproteinase. Phys Chem Chem Phys 2018; 19:30316-30331. [PMID: 28951896 DOI: 10.1039/c7cp05572b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Matrix metalloproteinases (MMP) are an important family of proteases which catalyze the degradation of extracellular matrix components. While the mechanism of peptide cleavage is well established, the process of enzyme regeneration, which represents the rate limiting step of the catalytic cycle, remains unresolved. This step involves the loss of the newly formed N-terminus (amine) and C-terminus (carboxylate) protein fragments from the site of catalysis coupled with the inclusion of one or more solvent waters. Here we report a novel crystal structure of membrane type I MMP (MT1-MMP or MMP-14), which includes a small peptide bound at the catalytic Zn site via its C-terminus. This structure models the initial product state formed immediately after peptide cleavage but before the final proton transfer to the bound amine; the amine is not present in our system and as such proton transfer cannot occur. Modeling of the protein, including earlier structural data of Bertini and coworkers [I. Bertini, et al., Angew. Chem., Int. Ed., 2006, 45, 7952-7955], suggests that the C-terminus of the peptide is positioned to form an H-bond network to the amine site, which is mediated by a single oxygen of the functionally important Glu240 residue, facilitating efficient proton transfer. Additional quantum chemical calculations complemented with magneto-optical and magnetic resonance spectroscopies clarify the role of two additional, non-catalytic first coordination sphere waters identified in the crystal structure. One of these auxiliary waters acts to stabilize key intermediates of the reaction, while the second is proposed to facilitate C-fragment release, triggered by protonation of the amine. Together these results complete the enzymatic cycle of MMPs and provide new design criteria for inhibitors with improved efficacy.
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Affiliation(s)
- Elena Decaneto
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße. 34-36, D-45470, Mülheim an der Ruhr, Germany.
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An integrated computational approach to rationalize the activity of non-zinc-binding MMP-2 inhibitors. PLoS One 2012; 7:e47774. [PMID: 23144829 PMCID: PMC3493580 DOI: 10.1371/journal.pone.0047774] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/17/2012] [Indexed: 11/29/2022] Open
Abstract
Matrix metalloproteinases are a family of Zn-proteases involved in tissue remodeling and in many pathological conditions. Among them MMP-2 is one of the most relevant target in anticancer therapy. Commonly, MMP inhibitors contain a functional group able to bind the zinc ion and responsible for undesired side effects. The discovery of potent and selective MMP inhibitors not bearing a zinc-binding group is arising for some MMP family members and represents a new opportunity to find selective and non toxic inhibitors. In this work we attempted to get more insight on the inhibition process of MMP-2 by two non-zinc-binding inhibitors, applying a general protocol that combines several computational tools (docking, Molecular Dynamics and Quantum Chemical calculations), that all together contribute to rationalize experimental inhibition data. Molecular Dynamics studies showed both structural and mechanical-dynamical effects produced by the ligands not disclosed by docking analysis. Thermodynamic Integration provided relative binding free energies consistent with experimentally observed activity data. Quantum Chemical calculations of the tautomeric equilibrium involving the most active ligand completed the picture of the binding process. Our study highlights the crucial role of the specificity loop and suggests that enthalpic effect predominates over the entropic one.
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Wang J, Zhang W, Yi Z, Wang S, Li Z. Identification of a thrombin cleavage site and a short form of ADAMTS-18. Biochem Biophys Res Commun 2012; 419:692-7. [PMID: 22386991 PMCID: PMC3313623 DOI: 10.1016/j.bbrc.2012.02.081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 02/14/2012] [Indexed: 12/20/2022]
Abstract
We previously reported that C-terminal fragment of ADAMTS-18 induces platelet fragmentation through ROS release. We have shown that thrombin cleaves ADAMTS-18 and that a short form of ADAMTS-18 in in vitro translational assay. However, the exact thrombin cleavage site and whether a short form ADAMTS-18 presents in vivo are not clear. In this study, we first identified that the thrombin cleavage site is between Arg775 and Ser776 by thrombin cleavage of ADAMTS-18 peptide following mass spectrum assay. We then showed that a short form ADAMTS-18 presents in brain, kidney, lung, and testicle from C57BL/6 mouse embryo. Since alternative form of ADAMTS-18 could be a mechanism to regulate its activity, we then investigated the mechanism involves in the generation of ADAMTS-18 short form. However, neither protease inhibitors nor mutations in catalytic domain of ADAMTS-18 have any significant effect on the generation of ADAMTS-18 short form. Thus, our data demonstrate a thrombin cleavage site and confirm a short form of ADAMTS-18 presents in vivo.
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Affiliation(s)
- Jianhui Wang
- Department of Medicine, NYU Cancer Institute, New York University School of Medicine 550 First Avenue New York, NY 10016
| | - Wei Zhang
- Department of Medicine, NYU Cancer Institute, New York University School of Medicine 550 First Avenue New York, NY 10016
| | - Zanhua Yi
- Department of Medicine, NYU Cancer Institute, New York University School of Medicine 550 First Avenue New York, NY 10016
| | - Shiyang Wang
- Department of Medicine, NYU Cancer Institute, New York University School of Medicine 550 First Avenue New York, NY 10016
| | - Zongdong Li
- Department of Medicine, NYU Cancer Institute, New York University School of Medicine 550 First Avenue New York, NY 10016
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7
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Morishima A, Yasukawa K, Inouye K. A possibility of a protein-bound water molecule as the ionizable group responsible for pKe at the alkaline side in human matrix metalloproteinase 7 activity. J Biochem 2012; 151:501-9. [PMID: 22368250 DOI: 10.1093/jb/mvs016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human matrix metalloproteinase 7 (MMP-7) activity exhibits broad bell-shaped pH profile with the acidic and alkaline pK(a) (pK(e1) and pK(e2)) values of about 4 and 10. The ionizable group for pK(e2) was assigned to Lys or Arg by thermodynamic analysis; however, no such residues are present in the active site. Hence, based on the crystal structure, we hypothesized that a water molecule bound to the main-chain nitrogen of Ala162 (W1) or the main-chain carbonyl oxygen of Pro217 (W2) is a candidate for the ionizable group for pK(e2) [Takeharu, H. et al. (2011) Biochim. Biophys. Acta 1814, 1940-1946]. In this study, we inspected this hypothesis. In the hydrolysis of (7-methoxycoumarin-4-yl)acetyl-L-Pro-L-Leu-Gly-L-Leu-[N(3)-(2,4-dinitrophenyl)-L-2,3-diaminopropionyl]-L-Ala-L-Arg-NH(2), all 19 variants, in which one of all Lys and Arg residues was replaced by Ala, retained activity, indicating that neither Lys nor Arg is the ionizable group. pK(e2) values of A162S, A162V and A162G were 9.6 ± 0.1, 9.5 ± 0.1 and 10.4 ± 0.2, respectively, different from that of wild-type MMP-7 (WT) (9.9 ± 0.1) by 0.3-0.5 pH unit, and those of P217S, P217V and P217G were 10.1 ± 0.1, 9.8 ± 0.1 and 9.7 ± 0.1, respectively, different from that of WT by 0.1-0.2 pH unit. These results suggest a possibility of W1 or W2 as the ionizable group for pK(e2).
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Affiliation(s)
- Aiko Morishima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Takeharu H, Yasukawa K, Inouye K. Thermodynamic analysis of ionizable groups involved in the catalytic mechanism of human matrix metalloproteinase 7 (MMP-7). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1940-6. [DOI: 10.1016/j.bbapap.2011.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 07/09/2011] [Accepted: 07/11/2011] [Indexed: 12/27/2022]
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Díaz N, Suárez D. Peptide hydrolysis catalyzed by matrix metalloproteinase 2: a computational study. J Phys Chem B 2008; 112:8412-24. [PMID: 18570467 DOI: 10.1021/jp803509h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The MMP-2 reaction mechanism is investigated by using different computational methodologies. First, quantum mechanical (QM) calculations are carried out on a cluster model of the active site bound to an Ace-Gly approximately Ile-Nme peptide. Along the QM reaction path, a Zn-bound water molecule attacks the Gly carbonyl group to give a tetrahedral intermediate. The breaking of the C-N bond is completed thanks to the Glu 404 residue that shuttles a proton from the water molecule to Ile-N atom. The gas-phase QM energy barrier is quite low ( approximately 14 kcal/mol), thus suggesting that the essential catalytic machinery is included in the cluster model. A similar reaction path occurs in the MMP-2 catalytic domain bound to an octapeptide substrate according to hybrid QM and molecular mechanical (QM/MM) geometry optimizations. However, the rupture of the Gly( P 1) approximately Ile( P 1') amide bond is destabilized in the static QM/MM calculations, owing to the positioning of the Ile( P 1') side chain inside the MMP-2 S 1' pocket and to the inability of simple energy miminization methodologies to properly relax complex systems. Molecular dynamics simulations show that these steric limitations are overcome easily through structural fluctuations. The energetic effect of structural fluctuations is taken into account by combining QM energies with average MM Poisson-Boltzmann free energies, resulting in a total free energy barrier of 14.8 kcal/mol in good agreement with experimental data. The rate-determining event in the MMP-2 mechanism corresponds to a H-bond rearrangement involving the Glu 404 residue and/or the Glu 404-COOH --> N-Ile( P 1') proton transfer. Overall, the present computational results and previous experimental data complement each other well in order to provide a detailed view of the MMPs catalytic mechanism.
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Affiliation(s)
- Natalia Díaz
- Departamento de Quimica Fisica y Analitica, Universidad de Oviedo. C/ Julian Claveria, 8, 33006, Oviedo (Asturias), Spain.
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10
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Díaz N, Suarez D. Molecular Dynamics Simulations of Matrix Metalloproteinase 2: Role of the Structural Metal Ions,. Biochemistry 2007; 46:8943-52. [PMID: 17616173 DOI: 10.1021/bi700541p] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we investigate the role played by the so-called "structural metal ions" in the catalytic domain of the matrix metalloproteinase 2 enzyme (MMP-2 or gelatinase A). We performed seven molecular dynamics simulations that differ in the number and position of the noncatalytic zinc and calcium ions bound to the MMP-2 catalytic domain. An additional simulation including the three fibronectin-type modules inserted into the catalytic domain was also carried out. The analysis of the trajectories confirms that the binding/removal of the structural ions does not perturb the secondary structure elements but influences the position of several solvent-exposed loop regions that are placed near the active site cleft. The position of these loops modulates the accessibility of important anchorage points for substrate binding that have been identified in the active site groove. On the basis of semiempirical quantum chemical calculations, we estimated the relative free energies of the MMP-2 models, obtaining thus that the binding of two zinc and two calcium ions to the MMP-2 catalytic domain is energetically favored. In this MMP-2 model, which shows the most compact structure, all of the substrate binding sites are readily accessible. Globally, our results help to rationalize at the atomic level the calcium and zinc dependence of the hydrolytic activity catalyzed by the MMPs.
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Affiliation(s)
- Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, C/JuliAn Clavería, 8. 33006, Oviedo (Asturias), Spain.
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Díaz N, Suarez D, Sordo TL. Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases. J Phys Chem B 2007; 110:24222-30. [PMID: 17125395 DOI: 10.1021/jp0656882] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
X-ray analyses of matrix metalloproteinases (MMPs) have shown that the catalytic zinc ion (Zn1) can bind to one to three water molecules in addition to three conserved histidine residues. To estimate the relative stability of the possible Zn1 coordination structures in the active site of the MMPs, we carry out computational analyses on the coordination environment of the Zn1 ion in the gelatinase A enzyme (or matrix metalloproteinase 2; MMP-2). Four-, five-, and six-coordinated complexes representative of the Zn1 site are fully characterized by means of quantum mechanical (QM) methodologies. On one hand, B3LYP/LACVP* minimizations of various cluster models of the MMP-2 active site show that the trigonal bipyramidal geometry is energetically favored in the gas phase and that continuum solvent effects stabilize preferentially the tetrahedral complexes. On the other hand, B3LYP/OPLS-AA hybrid QM/molecular mechanical calculations in the solvated catalytic domain of the MMP-2 enzyme complemented with electrostatic Poisson-Boltzmann calculations show that the mature enzyme presents most likely a Zn1 ion coordinated by three histidine residues and two water molecules, while the active site glutamic acid is negatively charged. In consonance with X-ray diffraction data, other possible Zn1 configurations, a six-coordinated structure with Zn1-water as well as four- and five-coordinated complexes with a Zn1-bound hydroxide, are predicted to be very close in energy.
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Affiliation(s)
- Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo C/Julián Clavería 8, 33006 Oviedo (Asturias), Spain.
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Si-Tayeb K, Monvoisin A, Mazzocco C, Lepreux S, Decossas M, Cubel G, Taras D, Blanc JF, Robinson DR, Rosenbaum J. Matrix metalloproteinase 3 is present in the cell nucleus and is involved in apoptosis. THE AMERICAN JOURNAL OF PATHOLOGY 2006; 169:1390-401. [PMID: 17003494 PMCID: PMC1780186 DOI: 10.2353/ajpath.2006.060005] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Matrix metalloproteinase (MMP)-3 is a protease involved in cancer progression and tissue remodeling. Using immunofluorescence and immunoelectron microscopy, we identified nuclear localization of MMP-3 in several cultured cell types and in human liver tissue sections. Western blot analysis of nuclear extracts revealed two immunoreactive forms of MMP-3 at 35 and 45 kd, with the 35-kd form exhibiting caseinolytic activity. By transient transfection, we expressed active MMP-3 fused to the enhanced green fluorescent protein (EGFP/aMMP-3) in Chinese hamster ovary cells. We showed that EGFP/aMMP-3 translocates into the nucleus. A functional nuclear localization signal was demonstrated by the loss of nuclear translocation after site-directed mutagenesis of a putative nuclear localization signal and by the ability of the MMP-3 nuclear localization signal to drive a heterologous protein into the nucleus. Finally, expression by Chinese hamster ovary cells of EGFP/aMMP-3 induced a twofold increase of apoptosis rate, compared with EGFP/pro-MMP-3, which does not translocate to the nucleus. Increased apoptosis was abolished by site-directed mutagenesis of the catalytic site of MMP-3 or by using the MMP inhibitor GM6001. This study elucidates for the first time the mechanisms of nuclear localization of a MMP and shows that nuclear MMP-3 can induce apoptosis via its catalytic activity.
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Affiliation(s)
- Karim Si-Tayeb
- INSERM E362, Université Victor Segalen Bordeaux 2, 33076 Bordeaux, France
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Chang HT, Pai TW, Fan TC, Su BH, Wu PC, Tang CY, Chang CT, Liu SH, Chang MDT. A reinforced merging methodology for mapping unique peptide motifs in members of protein families. BMC Bioinformatics 2006; 7:38. [PMID: 16433931 PMCID: PMC1369005 DOI: 10.1186/1471-2105-7-38] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 01/25/2006] [Indexed: 01/11/2023] Open
Abstract
Background Members of a protein family often have highly conserved sequences; most of these sequences carry identical biological functions and possess similar three-dimensional (3-D) structures. However, enzymes with high sequence identity may acquire differential functions other than the common catalytic ability. It is probable that each of their variable regions consists of a unique peptide motif (UPM), which selectively interacts with other cellular proteins, rendering additional biological activities. The ability to identify and localize such UPMs is paramount in recognizing the characteristic role of each member of a protein family. Results We have developed a reinforced merging algorithm (RMA) with which non-gapped UPMs were identified in a variety of query protein sequences including members of human ribonuclease A (RNaseA), epidermal growth factor receptor (EGFR), matrix metalloproteinase (MMP), and Sma-and-Mad related protein families (Smad). The UPMs generally occupy specific positions in the resolved 3-D structures, especially the loop regions on the structural surfaces. These motifs coincide with the recognition sites for antibodies, as the epitopes of four monoclonal antibodies and two polyclonal antibodies were shown to overlap with the UPMs. Most of the UPMs were found to correlate well with the potential antigenic regions predicted by PROTEAN. Furthermore, an accuracy of 70% can be achieved in terms of mapping a UPM to an epitope. Conclusion Our study provides a bioinformatic approach for searching and predicting potential epitopes and interacting motifs that distinguish different members of a protein family.
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Affiliation(s)
- Hao-Teng Chang
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, 30013, ROC, Taiwan
| | - Tun-Wen Pai
- Department of Computer Science, National Taiwan Ocean University, Keelung, 20224, ROC, Taiwan
| | - Tan-chi Fan
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, 30013, ROC, Taiwan
| | - Bo-Han Su
- Department of Computer Science, National Taiwan Ocean University, Keelung, 20224, ROC, Taiwan
| | - Pei-Chih Wu
- Department of Computer Science, National Taiwan Ocean University, Keelung, 20224, ROC, Taiwan
| | - Chuan-Yi Tang
- Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, ROC, Taiwan
| | - Chun-Tien Chang
- Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, ROC, Taiwan
| | - Shi-Hwei Liu
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, 30013, ROC, Taiwan
| | - Margaret Dah-Tsyr Chang
- Institute of Molecular and Cellular Biology & Department of Life Science, National Tsing Hua University, Hsinchu, 30013, ROC, Taiwan
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Pelmenschikov V, Siegbahn PEM. Catalytic mechanism of matrix metalloproteinases: two-layered ONIOM study. Inorg Chem 2002; 41:5659-66. [PMID: 12401069 DOI: 10.1021/ic0255656] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The two-layered ONIOM(B3LYP:MNDO) method has been used to investigate the hydrolytical mechanism of matrix metalloproteinases (MMPs), a large family of zinc-dependent endopeptidases capable of degrading a wide range of macromolecules of the extracellular matrix. Human stromelysin-1 (MMP-3) was chosen as a physiologically important member of the MMP family. As a structural reference, X-ray data on the stromelysin-1 catalytic domain (SCD) complexed to the transition state analogue diphenyl piperidine sulfonamide inhibitor was used. The backbone spacer of 11 residues (201-211) was included in the final model, spanning the catalytic Glu202 residue and the three structural His201,205,211 zinc ligands. The polypeptide framework incorporated, partly accounting for the protein rigidity, reduces the activation free energy slightly by 1.6 kcal/mol. Essentially a single-step catalytic mechanism was obtained, generally following a classical proposal for MMPs. Glu202 here acts as a base, abstracting a proton from the metal-bound reactant water and delivering this proton to the peptide nitrogen. An auxiliary water molecule is suggested to be of crucial importance acting as an electrophilic agent to the carbonyl oxygen of the substrate. The direct inclusion of the auxiliary water molecule decreases the activation free energy by about 5 kcal/mol via donation of a strong hydrogen bond. The calculated activation barrier of 13.1 kcal/mol agrees well with experimental rates.
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Affiliation(s)
- Vladimir Pelmenschikov
- Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology (SCFAB), Stockholm University, S-106 91 Stockholm, Sweden
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15
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Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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