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Wang RR, Ma Y, Du S, Li WY, Sun YZ, Zhou H, Wang RL. Exploring the reason for increased activity of SHP2 caused by D61Y mutation through molecular dynamics. Comput Biol Chem 2019; 78:133-143. [DOI: 10.1016/j.compbiolchem.2018.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 01/01/2023]
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Majumder DR, Kanekar PP. Proteases from Thermophiles and Their Industrial Importance. Ind Biotechnol (New Rochelle N Y) 2017. [DOI: 10.1201/9781315366562-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Proteases from Thermophiles and Their Industrial Importance. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1201/b19347-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Adekoya OA, Sjøli S, Wuxiuer Y, Bilto I, Marques SM, Santos MA, Nuti E, Cercignani G, Rossello A, Winberg JO, Sylte I. Inhibition of pseudolysin and thermolysin by hydroxamate-based MMP inhibitors. Eur J Med Chem 2014; 89:340-8. [PMID: 25462250 DOI: 10.1016/j.ejmech.2014.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 09/30/2014] [Accepted: 10/04/2014] [Indexed: 11/24/2022]
Abstract
In the present study, we have investigated the inhibition of thermolysin and pseudolysin by a series of compounds previously identified as matrix metalloproteinase (MMP) inhibitors using experimental binding studies and theoretical calculations. The experimental studies showed that some of the compounds were able to inhibit thermolysin and pseudolysin in the low μM range. The studies revealed that, in general, the compounds bound in the order MMPs > pseudolysin > thermolysin, and the strongest pseudolysin and thermolysin binders were compounds 8-12. Furthermore, compounds 8 and 9 were unique in that they bound much stronger to the two bacterial enzymes than to the MMPs. The docking calculations suggested that the phenyl group of the strongest binders (compounds 8 and 9) occupy the S2(')-subpocket, while a second ring system occupy the S1-subpocket in both thermolysin and pseudolysin. When the compounds possess two ring systems, the largest and most electron rich ring system seems to occupy the S1-subpocket.
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Affiliation(s)
- Olayiwola A Adekoya
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Stian Sjøli
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Yimingjiang Wuxiuer
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Irina Bilto
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Sérgio M Marques
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - M Amélia Santos
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Elisa Nuti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Giovanni Cercignani
- Dipartimento di Biologia, Unità di Biochimica, Università di Pisa, Via San Zeno 51, 56127 Pisa, Italy
| | - Armando Rossello
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Jan-Olof Winberg
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway
| | - Ingebrigt Sylte
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, NO-9037 Tromsø, Norway.
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Kumar A, Zhang KYJ. Computational Investigation of SENP:SUMO Protein-Protein Interaction for Structure Based Drug Design. Mol Inform 2013; 32:267-80. [PMID: 27481522 DOI: 10.1002/minf.201200124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 02/05/2013] [Indexed: 11/11/2022]
Abstract
SUMO specific proteases (SENPs) are cysteine proteases that carry out the proteolytic processing of SUMO from its pro form as well as its deconjugation from substrate proteins. SENPs have been implicated in various cancers including prostate cancer, thyroid cancer and colon cancer. Therefore, the inhibition of SENPs is an attractive strategy for the treatment of cancer. However, the current SENP inhibitor development strategies target catalytic site and involve the usage of reactive functionalities to facilitate the covalent binding with a catalytic cysteine, which makes them less desirable for therapeutic purposes. Based on the available structural knowledge about the interaction of SENPs with various SUMO paralogues, an alternative approach for inhibiting SENPs could be via targeting SENP:SUMO protein-protein interaction. Here we have investigated the protein-protein interaction between SENP and SUMO as a target for structure based drug design using pocket prediction, ligand binding hotspot mapping, molecular dynamics simulation and in silico alanine mutagenesis. Finally, we have provided recommendations for the structure based design of SENP:SUMO protein-protein interaction inhibitors. Our study indicates that the SENP inhibitors targeting SENP:SUMO protein-protein interaction is a viable alternative strategy to existing inhibitors targeting the enzymatic site.
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Affiliation(s)
- Ashutosh Kumar
- Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan phone: +81-48-467-8792, fax: +81-48-467-8790
| | - Kam Y J Zhang
- Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan phone: +81-48-467-8792, fax: +81-48-467-8790.
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Dedachi K, Hirakawa T, Fujita S, Khan MTH, Sylte I, Kurita N. Specific interactions and binding free energies between thermolysin and dipeptides: Molecular simulations combined with Ab initio molecular orbital and classical vibrational analysis. J Comput Chem 2011; 32:3047-57. [DOI: 10.1002/jcc.21887] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 06/18/2011] [Accepted: 06/18/2011] [Indexed: 11/11/2022]
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Kantyka T, Rawlings ND, Potempa J. Prokaryote-derived protein inhibitors of peptidases: A sketchy occurrence and mostly unknown function. Biochimie 2010; 92:1644-56. [PMID: 20558234 DOI: 10.1016/j.biochi.2010.06.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 06/08/2010] [Indexed: 11/28/2022]
Abstract
In metazoan organisms protein inhibitors of peptidases are important factors essential for regulation of proteolytic activity. In vertebrates genes encoding peptidase inhibitors constitute up to 1% of genes reflecting a need for tight and specific control of proteolysis especially in extracellular body fluids. In stark contrast unicellular organisms, both prokaryotic and eukaryotic consistently contain only few, if any, genes coding for putative peptidase inhibitors. This may seem perplexing in the light of the fact that these organisms produce large numbers of proteases of different catalytic classes with the genes constituting up to 6% of the total gene count with the average being about 3%. Apparently, however, a unicellular life-style is fully compatible with other mechanisms of regulation of proteolysis and does not require protein inhibitors to control their intracellular and extracellular proteolytic activity. So in prokaryotes occurrence of genes encoding different types of peptidase inhibitors is infrequent and often scattered among phylogenetically distinct orders or even phyla of microbiota. Genes encoding proteins homologous to alpha-2-macroglobulin (family I39), serine carboxypeptidase Y inhibitor (family I51), alpha-1-peptidase inhibitor (family I4) and ecotin (family I11) are the most frequently represented in Bacteria. Although several of these gene products were shown to possess inhibitory activity, with an exception of ecotin and staphostatins, the biological function of microbial inhibitors is unclear. In this review we present distribution of protein inhibitors from different families among prokaryotes, describe their mode of action and hypothesize on their role in microbial physiology and interactions with hosts and environment.
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Affiliation(s)
- Tomasz Kantyka
- Department of Microbiology, Jagiellonian University, Krakow, Poland
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Dedachi K, Khan MTH, Sylte I, Kurita N. A combined simulation with ab initio MO and classical vibrational analysis on the specific interactions between thermolysin and dipeptide ligands. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.08.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Olufsen M, Smalås AO, Brandsdal BO. Electrostatic interactions play an essential role in DNA repair and cold-adaptation of uracil DNA glycosylase. J Mol Model 2008; 14:201-13. [PMID: 18196298 DOI: 10.1007/s00894-007-0261-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 12/03/2007] [Indexed: 01/01/2023]
Abstract
Life has adapted to most environments on earth, including low and high temperature niches. The increased catalytic efficiency and thermoliability observed for enzymes from organisms living in constantly cold regions when compared to their mesophilic and thermophilic cousins are poorly understood at the molecular level. Uracil DNA glycosylase (UNG) from cod (cUNG) catalyzes removal of uracil from DNA with an increased k(cat) and reduced K(m) relative to its warm-active human (hUNG) counterpart. Specific issues related to DNA repair and substrate binding/recognition (K(m)) are here investigated by continuum electrostatics calculations, MD simulations and free energy calculations. Continuum electrostatic calculations reveal that cUNG has surface potentials that are more complementary to the DNA potential at and around the catalytic site when compared to hUNG, indicating improved substrate binding. Comparative MD simulations combined with free energy calculations using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method show that large opposing energies are involved when forming the enzyme-substrate complexes. Furthermore, the binding free energies obtained reveal that the Michaelis-Menten complex is more stable for cUNG, primarily due to enhanced electrostatic properties, suggesting that energetic fine-tuning of electrostatics can be utilized for enzymatic temperature adaptation. Energy decomposition pinpoints the residual determinants responsible for this adaptation.
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Affiliation(s)
- Magne Olufsen
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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Zhang Q, Schlick T. Stereochemistry and position-dependent effects of carcinogens on TATA/TBP binding. Biophys J 2006; 90:1865-77. [PMID: 16387764 PMCID: PMC1386768 DOI: 10.1529/biophysj.105.074344] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 11/21/2005] [Indexed: 01/25/2023] Open
Abstract
The TATA-box binding protein (TBP) is required by eukaryotic RNA polymerases to bind to the TATA box, an eight-basepair DNA promoter element, to initiate transcription. Carcinogen adducts that bind to the TATA box can hamper this important process. Benzo[a]pyrene (BP) is a representative chemical carcinogen that can be metabolically converted to highly reactive benzo[a]pyrene diol epoxides (BPDE), which in turn can form chemically stereoisomeric BP-DNA adducts. Depending on the TATA-bound adduct's location and stereochemistry, TATA/TBP binding can be decreased or increased. Our previous study interpreted the location-dependent effect in terms of conformational freedom and major-groove space available to BP. Here we further explore specific structural changes of the TATA/TBP complex to help interpret the stereochemical effect in terms of the flexibility of the TATA bases that frame the intercalated adduct. Thermodynamic analyses using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) yield large standard deviations, which make the computed binding free energies the same within the error bars and point to current limitations of free energy calculations of large and highly charged systems like DNA/protein complexes.
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Affiliation(s)
- Qing Zhang
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York, USA
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Adekoya OA, Willassen NP, Sylte I. Molecular insight into pseudolysin inhibition using the MM-PBSA and LIE methods. J Struct Biol 2006; 153:129-44. [PMID: 16376106 DOI: 10.1016/j.jsb.2005.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2005] [Revised: 11/03/2005] [Accepted: 11/04/2005] [Indexed: 11/23/2022]
Abstract
Pseudolysin, the extracellullar elastase of Pseudomonas aeruginosa (EC: 3.4.24.26) plays an important role in the pathogenesis of P. aeruginosa infections. In the present study, molecular dynamics simulations and theoretical affinity predictions were used to gain molecular insight into pseudolysin inhibition. Four low molecular weight inhibitors were docked at their putative binding sites and molecular dynamics (MD) simulations were performed for 5.0 ns, and the free energy of binding was calculated by the linear interaction energy method. The number and the contact surface area of stabilizing hydrophobic, aromatic, and hydrogen bonding interactions appears to reflect the affinity differences between the inhibitors. The proteinaceous inhibitor, Streptomyces metalloproteinase inhibitor (SMPI) was docked in three different binding positions and MD simulations were performed for 3.0 ns. The MD trajectories were used for molecular mechanics-Poisson-Boltzmann surface area analysis of the three binding positions. Computational alanine scanning of the average pseudolysin-SMPI complexes after MD revealed residues at the pseudolysin-SMPI interface giving the main contribution to the free energy of binding. The calculations indicated that SMPI interacts with pseudolysin via the rigid active site loop, but that also contact sites outside this loop contribute significantly to the free energy of association.
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Affiliation(s)
- Olayiwola A Adekoya
- Department of Pharmacology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, N-9037 Tromsø, Norway
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Adekoya OA, Helland R, Willassen NP, Sylte I. Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family. Proteins 2005; 62:435-49. [PMID: 16294337 DOI: 10.1002/prot.20773] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Knowledge about the structural features underlying cold adaptation is important for designing enzymes of different industrial relevance. Vibriolysin from Antarctic bacterium strain 643 (VAB) is at present the only enzyme of the thermolysin family from an organism that thrive in extremely cold climate. In this study comparative sequence-structure analysis and molecular dynamics (MD) simulations were used to reveal the molecular features of cold adaptation of VAB. Amino acid sequence analysis of 44 thermolysin enzymes showed that VAB compared to the other enzymes has: (1) fewer arginines, (2) a lower Arg/(Lys + Arg) ratio, (3) a lower fraction of large aliphatic side chains, expressed by the (Ile + Leu)/(Ile + Leu + Val) ratio, (4) more methionines, (5) more serines, and (6) more of the thermolabile amino acid asparagine. A model of the catalytic domain of VAB was constructed based on homology with pseudolysin. MD simulations for 3 ns of VAB, pseudolysin, and thermolysin supported the assumption that cold-adapted enzymes have a more flexible three-dimensional (3D) structure than their thermophilic and mesophilic counterparts, especially in some loop regions. The structural analysis indicated that VAB has fewer intramolecular cation-pi electron interactions and fewer hydrogen bonds than its mesophilic (pseudolysin) and thermophilic (thermolysin) counterparts. Lysine is the dominating cationic amino acids involved in salt bridges in VAB, while arginine is dominating in thermolysin and pseudolysin. VAB has a greater volume of inaccessible cavities than pseudolysin and thermolysin. The electrostatic potentials on the surface of the catalytic domain were also more negative for VAB than for thermolysin and pseudolysin. Thus, the MD simulations, the structural patterns, and the amino acid composition of VAB relative to other enzymes of the thermolysin family suggest that VAB possesses the biophysical properties generally following adaptation to cold climate.
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Affiliation(s)
- Olayiwola A Adekoya
- Department of Pharmacology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, Tromsø, Norway
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