1
|
Vinces TC, de Souza AS, Carvalho CF, Visnardi AB, Teixeira RD, Llontop EE, Bismara BAP, Vicente EJ, Pereira JO, de Souza RF, Yonamine M, Marana SR, Farah CS, Guzzo CR. Monomeric Esterase: Insights into Cooperative Behavior, Hysteresis/Allokairy. Biochemistry 2024; 63:1178-1193. [PMID: 38669355 DOI: 10.1021/acs.biochem.3c00668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Herein, we present a novel esterase enzyme, Ade1, isolated from a metagenomic library of Amazonian dark earths soils, demonstrating its broad substrate promiscuity by hydrolyzing ester bonds linked to aliphatic groups. The three-dimensional structure of the enzyme was solved in the presence and absence of substrate (tributyrin), revealing its classification within the α/β-hydrolase superfamily. Despite being a monomeric enzyme, enzymatic assays reveal a cooperative behavior with a sigmoidal profile (initial velocities vs substrate concentrations). Our investigation brings to light the allokairy/hysteresis behavior of Ade1, as evidenced by a transient burst profile during the hydrolysis of substrates such as p-nitrophenyl butyrate and p-nitrophenyl octanoate. Crystal structures of Ade1, coupled with molecular dynamics simulations, unveil the existence of multiple conformational structures within a single molecular state (E̅1). Notably, substrate binding induces a loop closure that traps the substrate in the catalytic site. Upon product release, the cap domain opens simultaneously with structural changes, transitioning the enzyme to a new molecular state (E̅2). This study advances our understanding of hysteresis/allokairy mechanisms, a temporal regulation that appears more pervasive than previously acknowledged and extends its presence to metabolic enzymes. These findings also hold potential implications for addressing human diseases associated with metabolic dysregulation.
Collapse
Affiliation(s)
- Tania Churasacari Vinces
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Cecília F Carvalho
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Aline Biazola Visnardi
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Raphael D Teixeira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Edgar E Llontop
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Beatriz Aparecida Passos Bismara
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Elisabete J Vicente
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - José O Pereira
- Biotechnology Group, Federal University of Amazonas, Amazonas CEP 69077-000, Brazil
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Mauricio Yonamine
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Sandro Roberto Marana
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Chuck Shaker Farah
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo CEP 05508-000, Brazil
| | - Cristiane R Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP 05508-000, Brazil
| |
Collapse
|
2
|
Ferreira GM, Kronenberger T, Maltarollo VG, Poso A, de Moura Gatti F, Almeida VM, Marana SR, Lopes CD, Tezuka DY, de Albuquerque S, da Silva Emery F, Trossini GHG. Trypanosoma cruzi Sirtuin 2 as a Relevant Druggable Target: New Inhibitors Developed by Computer-Aided Drug Design. Pharmaceuticals (Basel) 2023; 16:ph16030428. [PMID: 36986527 PMCID: PMC10057528 DOI: 10.3390/ph16030428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/17/2023] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, relies on finely coordinated epigenetic regulation during the transition between hosts. Herein we targeted the silent information regulator 2 (Sir2) enzyme, a NAD+-dependent class III histone deacetylase, to interfere with the parasites’ cell cycle. A combination of molecular modelling with on-target experimental validation was used to discover new inhibitors from commercially available compound libraries. We selected six inhibitors from the virtual screening, which were validated on the recombinant Sir2 enzyme. The most potent inhibitor (CDMS-01, IC50 = 40 μM) was chosen as a potential lead compound.
Collapse
Affiliation(s)
- Glaucio Monteiro Ferreira
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 13, São Paulo 05508-000, SP, Brazil; (G.M.F.)
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 17, São Paulo 05508-000, SP, Brazil
| | - Thales Kronenberger
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Vinicius Gonçalves Maltarollo
- Department of Pharmaceutical Products, Faculty of Pharmacy, Federal University of Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte 31270-901, MG, Brazil
| | - Antti Poso
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Fernando de Moura Gatti
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 13, São Paulo 05508-000, SP, Brazil; (G.M.F.)
| | - Vitor Medeiros Almeida
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av Prof Lineu Prestes 748, Building 12, São Paulo 05508-000, SP, Brazil; (V.M.A.)
| | - Sandro Roberto Marana
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av Prof Lineu Prestes 748, Building 12, São Paulo 05508-000, SP, Brazil; (V.M.A.)
| | - Carla Duque Lopes
- Department of Clinical Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
| | - Daiane Yukie Tezuka
- Department of Clinical Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
| | - Sérgio de Albuquerque
- Department of Clinical Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
| | - Flavio da Silva Emery
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
- Correspondence: (F.d.S.E.); (G.H.G.T.); Tel.: +55-11-3091-3793 (G.H.G.T.)
| | - Gustavo Henrique Goulart Trossini
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 13, São Paulo 05508-000, SP, Brazil; (G.M.F.)
- Correspondence: (F.d.S.E.); (G.H.G.T.); Tel.: +55-11-3091-3793 (G.H.G.T.)
| |
Collapse
|
3
|
Barbosa GR, Marana SR, Stolf BS. Characterization of Leishmania ( L.) amazonensis oligopeptidase B and its role in macrophage infection. Parasitology 2022; 149:1411-1418. [PMID: 35703092 PMCID: PMC11010554 DOI: 10.1017/s0031182022000816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/09/2022] [Accepted: 05/30/2022] [Indexed: 11/07/2022]
Abstract
Leishmania spp. are parasitic protozoa that cause leishmaniasis, a disease endemic in 98 countries. Leishmania promastigotes are transmitted by the vector and differentiate into amastigotes within phagocytic cells of the vertebrate host. To survive in multiple and hostile environments, the parasite has several virulence factors. Oligopeptidase B (OPB) is a serine peptidase present in prokaryotes, some eukaryotes and some higher plants. It has been considered a virulence factor in trypanosomatids, but only a few studies, performed with Old World species, analysed its role in Leishmania virulence or infectivity.L. (L.) amazonensis is an important agent of cutaneous leishmaniasis in Brazil. The L. (L.) amazonensis OPB encoding gene has been sequenced and analysed in silico but has never been expressed. In this work, we produced recombinant L. (L.) amazonensis OPB and showed that its pH preferences, Km and inhibition patterns are similar to those reported for L. (L.) major and L. (L.) donovani OPBs. Since Leishmania is known to secrete OPB, we performed in vitro infection assays using the recombinant enzyme. Our results showed that active OPB increased in vitro infection by L. (L.) amazonensis when present before and throughout infection. Our findings suggest that OPB is relevant to L. (L.) amazonensis infection, and that potential drugs acting through OPB will probably be effective for Old and New World Leishmania species. OPB inhibitors may eventually be explored for leishmaniasis chemotherapy.
Collapse
Affiliation(s)
- Gustavo Rolim Barbosa
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sandro Roberto Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Beatriz Simonsen Stolf
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
4
|
Medeiros Almeida V, Chaudhuri A, Cangussu Cardoso MV, Matsuyama BY, Monteiro Ferreira G, Goulart Trossini GH, Salinas RK, Loria JP, Marana SR. Role of a high centrality residue in protein dynamics and thermal stability. J Struct Biol 2021; 213:107773. [PMID: 34320379 DOI: 10.1016/j.jsb.2021.107773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/02/2021] [Accepted: 07/21/2021] [Indexed: 11/27/2022]
Abstract
Centralities determined from Residue Interaction Networks (RIN) in proteins have been used to predict aspects of their structure and dynamics. Here, we correlate the Eigenvector Centrality (Ec) with the rate constant for thermal denaturation (kden) of the HisF protein from Thermotoga maritima based on 12 single alanine substitution mutants. The molecular basis for this correlation was further explored by studying a mutant containing a replacement of a high Ec residue, Y182A, which displayed increased kden at 80 °C. The crystallographic structure of this mutant showed few changes, mostly in two flexible loops. The 1H-15N -HSQC showed only subtle changes of cross peak positions for residues located near the mutation site and scattered throughout the structure. However, the comparison of the RIN showed that Y182 is the vertex of a set of high centrality residues that spreads throughout the HisF structure, which is lacking in the mutant. Cross-correlation displacements of Cα calculated from a molecular dynamics simulation at different temperatures showed that the Y182A mutation reduced the correlated movements in the HisF structure above 70 °C. 1H-15N NMR chemical shift covariance using temperature as perturbation were consistent with these results. In conclusion the increase in temperature drives the structure of the mutant HisF-Y182A into a less connected state, richer in non-concerted motions, located predominantly in the C-terminal half of the protein where Y182 is placed. Conversely, wild-type HisF responds to increased temperature as a single unit. Hence the replacement of a high Ec residue alters the distribution of thermal energy through HisF structure.
Collapse
Affiliation(s)
- Vitor Medeiros Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Apala Chaudhuri
- Departament of Chemistry, Yale University, New Haven, CT, United States
| | | | - Bruno Yasui Matsuyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - Roberto Kopke Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - J Patrick Loria
- Departament of Chemistry, Yale University, New Haven, CT, United States; Departament of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Sandro Roberto Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
| |
Collapse
|
5
|
Silva de Souza A, Rivera JD, Almeida VM, Ge P, de Souza RF, Farah CS, Ulrich H, Marana SR, Salinas RK, Guzzo CR. Molecular Dynamics Reveals Complex Compensatory Effects of Ionic Strength on the Severe Acute Respiratory Syndrome Coronavirus 2 Spike/Human Angiotensin-Converting Enzyme 2 Interaction. J Phys Chem Lett 2020; 11:10446-10453. [PMID: 33269932 PMCID: PMC7737395 DOI: 10.1021/acs.jpclett.0c02602] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/30/2020] [Indexed: 05/13/2023]
Abstract
The SARS-CoV-2 pandemic has already killed more than one million people worldwide. To gain entry, the virus uses its Spike protein to bind to host hACE-2 receptors on the host cell surface and mediate fusion between viral and cell membranes. As initial steps leading to virus entry involve significant changes in protein conformation as well as in the electrostatic environment in the vicinity of the Spike/hACE-2 complex, we explored the sensitivity of the interaction to changes in ionic strength through computational simulations and surface plasmon resonance. We identified two regions in the receptor-binding domain (RBD), E1 and E2, which interact differently with hACE-2. At high salt concentration, E2-mediated interactions are weakened but are compensated by strengthening E1-mediated hydrophobic interactions. These results provide a detailed molecular understanding of Spike RBD/hACE-2 complex formation and stability under a wide range of ionic strengths.
Collapse
Affiliation(s)
- Anacleto Silva de Souza
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 5508-900 São Paulo, Brazil
| | - Jose David Rivera
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Vitor Medeiros Almeida
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Pingju Ge
- Acrobiosystems
Inc., Beijing 100176, China
| | - Robson Francisco de Souza
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 5508-900 São Paulo, Brazil
| | - Chuck Shaker Farah
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Henning Ulrich
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Sandro Roberto Marana
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Roberto Kopke Salinas
- Department
of Biochemistry, Institute of Chemistry, University of São Paulo, 05508-000 São Paulo, Brazil
| | - Cristiane Rodrigues Guzzo
- Department
of Microbiology, Institute of Biomedical Sciences, University of São Paulo, 5508-900 São Paulo, Brazil
| |
Collapse
|
6
|
Baptista MS, Alves MJM, Arantes GM, Armelin HA, Augusto O, Baldini RL, Basseres DS, Bechara EJH, Bruni-Cardoso A, Chaimovich H, Colepicolo Neto P, Colli W, Cuccovia IM, Da-Silva AM, Di Mascio P, Farah SC, Ferreira C, Forti FL, Giordano RJ, Gomes SL, Gueiros Filho FJ, Hoch NC, Hotta CT, Labriola L, Lameu C, Machini MT, Malnic B, Marana SR, Medeiros MHG, Meotti FC, Miyamoto S, Oliveira CC, Souza-Pinto NC, Reis EM, Ronsein GE, Salinas RK, Schechtman D, Schreier S, Setubal JC, Sogayar MC, Souza GM, Terra WR, Truzzi DR, Ulrich H, Verjovski-Almeida S, Winck FV, Zingales B, Kowaltowski AJ. Where do we aspire to publish? A position paper on scientific communication in biochemistry and molecular biology. ACTA ACUST UNITED AC 2019; 52:e8935. [PMID: 31482979 PMCID: PMC6719344 DOI: 10.1590/1414-431x20198935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/19/2019] [Indexed: 11/21/2022]
Abstract
The scientific publication landscape is changing quickly, with an enormous increase in options and models. Articles can be published in a complex variety of journals that differ in their presentation format (online-only or in-print), editorial organizations that maintain them (commercial and/or society-based), editorial handling (academic or professional editors), editorial board composition (academic or professional), payment options to cover editorial costs (open access or pay-to-read), indexation, visibility, branding, and other aspects. Additionally, online submissions of non-revised versions of manuscripts prior to seeking publication in a peer-reviewed journal (a practice known as pre-printing) are a growing trend in biological sciences. In this changing landscape, researchers in biochemistry and molecular biology must re-think their priorities in terms of scientific output dissemination. The evaluation processes and institutional funding for scientific publications should also be revised accordingly. This article presents the results of discussions within the Department of Biochemistry, University of São Paulo, on this subject.
Collapse
Affiliation(s)
- M S Baptista
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - M J M Alves
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - G M Arantes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - H A Armelin
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - O Augusto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - R L Baldini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - D S Basseres
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - E J H Bechara
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - A Bruni-Cardoso
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - H Chaimovich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - P Colepicolo Neto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - W Colli
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - I M Cuccovia
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - A M Da-Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - P Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S C Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - C Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - F L Forti
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - R J Giordano
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S L Gomes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - F J Gueiros Filho
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - N C Hoch
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - C T Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - L Labriola
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - C Lameu
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - M T Machini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - B Malnic
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S R Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - M H G Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - F C Meotti
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S Miyamoto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - C C Oliveira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - N C Souza-Pinto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - E M Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - G E Ronsein
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - R K Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - D Schechtman
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S Schreier
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - J C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - M C Sogayar
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - G M Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - W R Terra
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - D R Truzzi
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - H Ulrich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - S Verjovski-Almeida
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - F V Winck
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - B Zingales
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | - A J Kowaltowski
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| |
Collapse
|
7
|
Brognaro H, Almeida VM, de Araujo EA, Piyadov V, Santos MAM, Marana SR, Polikarpov I. Biochemical Characterization and Low-Resolution SAXS Molecular Envelope of GH1 β-Glycosidase from Saccharophagus degradans. Mol Biotechnol 2017; 58:777-788. [PMID: 27670285 DOI: 10.1007/s12033-016-9977-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The marine bacteria Saccharophagus degradans (also known as Microbulbifer degradans), are rod-shaped and gram-negative motile γ-proteobacteria, capable of both degrading a variety of complex polysaccharides and fermenting monosaccharides into ethanol. In order to obtain insights into structure-function relationships of the enzymes, involved in these biochemical processes, we characterized a S. degradans β-glycosidase from glycoside hydrolase family 1 (SdBgl1B). SdBgl1B has the optimum pH of 6.0 and a melting temperature T m of approximately 50 °C. The enzyme has high specificity toward short D-glucose saccharides with β-linkages with the following preferences β-1,3 > β-1,4 ≫ β-1,6. The enzyme kinetic parameters, obtained using artificial substrates p-β-NPGlu and p-β-NPFuc and also the disaccharides cellobiose, gentiobiose and laminaribiose, revealed SdBgl1B preference for p-β-NPGlu and laminaribiose, which indicates its affinity for glucose and also preference for β-1,3 linkages. To better understand structural basis of the enzyme activity its 3D model was built and analysed. The 3D model fits well into the experimentally retrieved low-resolution SAXS-based envelope of the enzyme, confirming monomeric state of SdBgl1B in solution.
Collapse
Affiliation(s)
- Hevila Brognaro
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil
| | - Vitor Medeiros Almeida
- Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 748, Bloco 10, Sala 1054, São Paulo, SP, 05508-900, Brazil
| | - Evandro Ares de Araujo
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil
| | - Vasily Piyadov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil
| | - Maria Auxiliadora Morim Santos
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil
| | - Sandro Roberto Marana
- Instituto de Química, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 748, Bloco 10, Sala 1054, São Paulo, SP, 05508-900, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400, São Carlos, SP, 13566-590, Brazil.
| |
Collapse
|
8
|
Frutuoso MA, Marana SR. A single amino acid residue determines the ratio of hydrolysis to transglycosylation catalyzed by β-glucosidases. Protein Pept Lett 2013; 20:102-106. [PMID: 22670763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 05/25/2012] [Accepted: 05/25/2012] [Indexed: 06/01/2023]
Abstract
The propensity to catalysis of transglycosylation of the β-glucosidase Tmβgly is higher than for Sfβgly. Moreover the propensity to catalysis of transglycosylation is directly proportional to the substrate concentration for Tmβgly, whereas for Sfβgly it is constant. For instance, 60% of a Tmβgly sample catalyzes transglycosylation reactions at 40 mM p-nitrophenyl β-glucoside, whereas only 40% is engaged in hydrolysis of this substrate. For Sfβgly the fraction involved in transglycosylation is only 30 %. In addition, 48 % of a Tmβgly sample catalyzes transglycosylation reactions at 8 mM methylumbelliferyl β-glucoside, whereas Sfβgly does not catalyze transglycosylation using this substrate. Interestingly, these Tmβgly properties were grafted into Sfβgly by a single replacement of a residue forming a channel involved in supplying the catalytic water molecules for attack on the covalent intermediate present in the reaction catalyzed by β-glucosidases. Hence a single residue determines the ratio of hydrolysis to transglycosylation reactions catalyzed by these β-glucosidases.
Collapse
Affiliation(s)
- M A Frutuoso
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brasil
| | | |
Collapse
|
9
|
Tomassi MH, Rozenfeld JHK, Gonçalves LM, Marana SR. Characterization of the interdependency between residues that bind the substrate in a beta-glycosidase. Braz J Med Biol Res 2009; 43:8-12. [PMID: 20027479 DOI: 10.1590/s0100-879x2009007500033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 11/27/2009] [Indexed: 11/22/2022] Open
Abstract
The manner by which effects of simultaneous mutations combine to change enzymatic activity is not easily predictable because these effects are not always additive in a linear manner. Hence, the characterization of the effects of simultaneous mutations of amino acid residues that bind the substrate can make a significant contribution to the understanding of the substrate specificity of enzymes. In the beta-glycosidase from Spodoptera frugiperda (Sfbetagly), both residues Q39 and E451 interact with the substrate and this is essential for defining substrate specificity. Double mutants of Sfbetagly (A451E39, S451E39 and S451N39) were prepared by site-directed mutagenesis, expressed in bacteria and purified using affinity chromatography. These enzymes were characterized using p-nitrophenyl beta-galactoside and p-nitrophenyl beta-fucoside as substrates. The k cat/Km ratio for single and double mutants of Sfbetagly containing site-directed mutations at positions Q39 and E451 was used to demonstrate that the effect on the free energy of ESdouble dagger (enzyme-transition state complex) of the double mutations (Gdouble daggerxy) is not the sum of the effects resulting from the single mutations (Gdouble daggerx and Gdouble daggery). This difference in Gdouble dagger indicates that the effects of the single mutations partially overlap. Hence, this common effect counts only once in Gdouble daggerxy. Crystallographic data on beta-glycosidases reveal the presence of a bidentate hydrogen bond involving residues Q39 and E451 and the same hydroxyl group of the substrate. Therefore, both thermodynamic and crystallographic data suggest that residues Q39 and E451 exert a mutual influence on their respective interactions with the substrate.
Collapse
Affiliation(s)
- M H Tomassi
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | | | | | | |
Collapse
|
10
|
Cançado FC, Valério AA, Marana SR, Barbosa JARG. The crystal structure of a lysozyme c from housefly Musca domestica, the first structure of a digestive lysozyme. J Struct Biol 2007; 160:83-92. [PMID: 17825580 DOI: 10.1016/j.jsb.2007.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 06/11/2007] [Accepted: 07/11/2007] [Indexed: 10/23/2022]
Abstract
Lysozymes from family 22 of glycoside hydrolases are usually part of the defense system against bacteria. However in ruminant artiodactyls and saprophagous insects, lysozymes are involved in the digestion of bacteria. Here, we report the first crystallographic structure of a digestive lysozyme in its native and complexed forms, the structure of lysozyme 1 from Musca domestica larvae midgut (MdL1). Structural and biochemical data presented for MdL1 are analyzed in light of digestive lysozymes' traits. The structural core is similar, but a careful analysis of a structural alignment generated with other lysozymes c reveals that significant differences occur in coil regions. The loop from MdL1 defined by residues 98-100 has one deletion previous to residue Gln100, which leads to a less exposed conformation and might justify the resistance to proteolysis observed for MdL1. In addition, Gln100 is directly involved in a few hydrogen bonds to the ligand in a yet unobserved substrate binding mode. The pK(a)s of the MdL1 catalytic residues (Glu32 and Asp50) are lower (6.40 and 3.09, respectively) than those from Gallus gallus egg lysozyme (GgL, hen egg white lysozyme-HEWL) (6.61 and 3.85, respectively). A unique feature of MdL1 is a hydrogen bond between Thr107 Ogamma and Glu32 carboxylate group, which combined with the presence of Ser106 contributes to decrease the pK(a) of Glu32. Furthermore, in MdL1 the presence of Asn46 preventing the occurrence of an electrostatic repulsion with Asp50 and the increment in the solvent exposition of Asp50 due to Pro42 insertion contribute to reduce the pK(a) of Asp50. These structural elements affecting the pK(a)s of the catalytic residues should contribute to the acidic pH optimum presented by MdL1.
Collapse
Affiliation(s)
- Fabiane Chaves Cançado
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, São Paulo, SP 05513-970, Brazil
| | | | | | | |
Collapse
|
11
|
Lopes AR, Juliano MA, Marana SR, Juliano L, Terra WR. Substrate specificity of insect trypsins and the role of their subsites in catalysis. Insect Biochem Mol Biol 2006; 36:130-40. [PMID: 16431280 DOI: 10.1016/j.ibmb.2005.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2005] [Revised: 11/11/2005] [Accepted: 11/17/2005] [Indexed: 05/06/2023]
Abstract
Trypsins have high sequence similarity, although the responses of insect trypsins to chemical and natural inhibitors suggest they differ in specificities. Purified digestive trypsins from insects of four different orders were assayed with internally quenched fluorescent oligopeptides with two different amino acids at P1 (Arg/Lys) and 15 amino acid replacements in positions P1', P2', P2, and P3. The binding energy (deltaG(s), calculated from Km values) and the activation energy (deltaG(T)(double dagger), determined from kcat/Km values) were calculated. Dictyoptera, Coleoptera and Diptera trypsins hydrolyze peptides with Arg at P1 at least 3 times more efficiently than peptides with Lys at P1, whereas Lepidoptera trypsins have no preference between Arg and Lys at that position. The hydrophobicities of each subsite were calculated from the efficiency of hydrolysis of the different amino acid replacements at that subsite. The results suggested that insect trypsin subsites become progressively more hydrophobic along evolution. Apparently, this is an adaptation to resist plant protein inhibitors, which usually have polar residues at their reactive sites. Results also suggested that, at least in lepidopteran trypsins, S3, S2, S1', and S2' significantly bind the substrate ground state, whereas in the transition state only S1' and S2' do that, supporting aspects of the presently accepted mechanism of trypsin catalysis. Homology modeling showed differences among those trypsins that may account for the varied kinetic properties.
Collapse
Affiliation(s)
- A R Lopes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, 05513-970 São Paulo, Brazil
| | | | | | | | | |
Collapse
|
12
|
Marana SR, Lopes AR, Juliano L, Juliano MA, Ferreira C, Terra WR. Subsites of trypsin active site favor catalysis or substrate binding. Biochem Biophys Res Commun 2002; 290:494-7. [PMID: 11779198 DOI: 10.1006/bbrc.2001.6172] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Enzymes enhance chemical reaction rates by lowering the activation energy, the energy barrier of the reaction leading to products. This occurs because enzymes bind the high-energy intermediate of the reaction (the transition state) more strongly than the substrate. We studied details of this process by determining the substrate binding energy (DeltaG(s), calculated from K(m) values) and the activation energy (DeltaG(T), determined from k(cat)/K(m) values) for the trypsin-catalyzed hydrolysis of oligopeptides. Plots of DeltaG(T) versus DeltaG(s) for oligopeptides with 15 amino acid replacements at each of the positions P(1)', P(1), and P(2) were straight lines, as predicted by a derived equation that relates DeltaG(T) and DeltaG(s). The data led to the conclusion that the trypsin active site has subsites that bind moieties of substrate and of transition state in characteristic ratios, whichever substrate is used. This was unexpected and means that each subsite characteristically favors substrate binding or catalysis.
Collapse
Affiliation(s)
- S R Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, CP 26077, São Paulo 05513-970, Brazil
| | | | | | | | | | | |
Collapse
|
13
|
Ferreira AH, Marana SR, Terra WR, Ferreira C. Purification, molecular cloning, and properties of a beta-glycosidase isolated from midgut lumen of Tenebrio molitor (Coleoptera) larvae. Insect Biochem Mol Biol 2001; 31:1065-1076. [PMID: 11520685 DOI: 10.1016/s0965-1748(01)00054-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Two beta-glycosidases (M(r) 59k) were purified from midgut contents of larvae of the yellow mealworm, Tenebrio molitor (Coleoptera: Tenebrionidae). The two enzymes (betaGly1 and betaGly2) have identical kinetic properties, but differ in hydrophobicity. The two glycosidases were cloned and their sequences differ by only four amino acids. The T. molitor glycosidases are family 1 glycoside hydrolases and have the E379 (nucleophile) and E169 (proton donor) as catalytic amino acids based on sequence alignments. The enzymes share high homology and similarity with other insect, mammalian and plant beta-glycosidases. The two enzymes may hydrolyze several substrates, such as disaccharides, arylglucosides, natural occurring plant glucosides, alkylglucosides, oligocellodextrins and the polymer laminarin. The enzymes have only one catalytic site, as inferred from experiments of competition between substrates and sequence alignments. The observed inhibition by high concentrations of the plant glucoside amygdalin, used as substrate, is an artifact generated by transglucosylation. The active site of each purified beta-glycosidase has four subsites, of which subsites +1 and +2 bind glucose with more affinity. Subsite +2 has more affinity for hydrophobic groups, binding with increasing affinities: glucose, mandelonitrile and nitrophenyl moieties. Subsite +3 has more affinity for glucose than butylene moieties. The intrinsic catalytic constant calculated for hydrolysis of the glucose beta-1,4-glucosidic bond is 21.2 s(-1) x M(-1). The putative physiological role of these enzymes is the digestion of di- and oligosaccharides derived from hemicelluloses.
Collapse
Affiliation(s)
- A H Ferreira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, C.P 26077, 05513-970, São Paulo, Brazil
| | | | | | | |
Collapse
|
14
|
Marana SR, Jacobs-Lorena M, Terra WR, Ferreira C. Amino acid residues involved in substrate binding and catalysis in an insect digestive beta-glycosidase. Biochim Biophys Acta 2001; 1545:41-52. [PMID: 11342030 DOI: 10.1016/s0167-4838(00)00260-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A beta-glycosidase (M(r) 50000) from Spodoptera frugiperda larval midgut was purified, cloned and sequenced. It is active on aryl and alkyl beta-glucosides and cellodextrins that are all hydrolyzed at the same active site, as inferred from experiments of competition between substrates. Enzyme activity is dependent on two ionizable groups (pK(a1)=4.9 and pK(a2)=7.5). Effect of pH on carbodiimide inactivation indicates that the pK(a) 7.5 group is a carboxyl. k(cat) and K(m) values were obtained for different p-nitrophenyl beta-glycosides and K(i) values were determined for a range of alkyl beta-glucosides and cellodextrins, revealing that the aglycone site has three subsites. Binding data, sequence alignments and literature beta-glycosidase 3D data supported the following conclusions: (1) the groups involved in catalysis were E(187) (proton donor) and E(399) (nucleophile); (2) the glycone moiety is stabilized in the transition state by a hydrophobic region around the C-6 hydroxyl and by hydrogen bonds with the other equatorial hydroxyls; (3) the aglycone site is a cleft made up of hydrophobic amino acids with a polar amino acid only at its first (+1) subsite.
Collapse
Affiliation(s)
- S R Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
| | | | | | | |
Collapse
|
15
|
Marana SR, Terra WR, Ferreira C. Purification and properties of a beta-glycosidase purified from midgut cells of Spodoptera frugiperda (Lepidoptera) larvae. Insect Biochem Mol Biol 2000; 30:1139-1146. [PMID: 11044660 DOI: 10.1016/s0965-1748(00)00090-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Two beta-glycosidases (BG) (Mr 47,000 and Mr 50,000) were purified from Spodoptera frugiperda (Lepidoptera: Noctuidae) midguts. These two polypeptides associate or dissociate depending on the medium ionic strength. The Mr 47,000 BG probably has two active sites. One of the putative active sites (cellobiase site) hydrolyses p-nitrophenyl beta-D-glucoside (NPbetaGlu) (79% of the total activity in saturated enzyme), cellobiose, amygdalin and probably also cellotriose, cellotetraose and cellopentaose. The cellobiase site has four subsites for glucose residue binding, as can be deduced from cellodextrin cleavage data. The enzymatic activity in this site is abolished after carbodiimide modification at pH 6.0. Since the inactivation is reduced in the presence of cellobiose, the results suggest the presence of a carboxylate as a catalytic group. The other active site of Mr 47,000 BG (galactosidase site) hydrolyses p-nitrophenyl beta-D-galactoside (NPbetaGal) better than NPbetaGlu, cleaves glucosylceramide and lactose and is unable to act on cellobiose, cellodextrins and amygdalin. This active site is not modified by carbodiimide at pH 6.0. The Mr 47,000 BG N-terminal sequence has high identity to plant beta-glycosidases and to mammalian lactase-phlorizin hydrolase, and contains the QIEGA motif, characteristic of the family of glycosyl hydrolases. The putative physiological role of this enzyme is the digestion of glycolipids (galactosidase site) and di- and oligosaccharides (cellobiase site) derived from hemicelluloses, thus resembling mammalian lactase-phlorizin hydrolase.
Collapse
Affiliation(s)
- S R Marana
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, C.P. 26077, 05513-970, São Paulo, Brazil
| | | | | |
Collapse
|