1
|
da Fonseca LM, da Costa KM, Chaves VDS, Freire-de-Lima CG, Morrot A, Mendonça-Previato L, Previato JO, Freire-de-Lima L. Theft and Reception of Host Cell's Sialic Acid: Dynamics of Trypanosoma Cruzi Trans-sialidases and Mucin-Like Molecules on Chagas' Disease Immunomodulation. Front Immunol 2019; 10:164. [PMID: 30787935 PMCID: PMC6372544 DOI: 10.3389/fimmu.2019.00164] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/18/2019] [Indexed: 12/27/2022] Open
Abstract
The last decades have produced a plethora of evidence on the role of glycans, from cell adhesion to signaling pathways. Much of that information pertains to their role on the immune system and their importance on the surface of many human pathogens. A clear example of this is the flagellated protozoan Trypanosoma cruzi, which displays on its surface a great variety of glycoconjugates, including O-glycosylated mucin-like glycoproteins, as well as multiple glycan-binding proteins belonging to the trans-sialidase (TS) family. Among the latter, different and concurrently expressed molecules may present or not TS activity, and are accordingly known as active (aTS) and inactive (iTS) members. Over the last thirty years, it has been well described that T. cruzi is unable to synthesize sialic acid (SIA) on its own, making use of aTS to steal the host's SIA. Although iTS did not show enzymatic activity, it retains a substrate specificity similar to aTS (α-2,3 SIA-containing glycotopes), displaying lectinic properties. It is accepted that aTS members act as virulence factors in mammals coursing the acute phase of the T. cruzi infection. However, recent findings have demonstrated that iTS may also play a pathogenic role during T. cruzi infection, since it modulates events related to adhesion and invasion of the parasite into the host cells. Since both aTS and iTS proteins share structural substrate specificity, it might be plausible to speculate that iTS proteins are able to assuage and/or attenuate biological phenomena depending on the catalytic activity displayed by aTS members. Since SIA-containing glycotopes modulate the host immune system, it should not come as any surprise that changes in the sialylation of parasite's mucin-like molecules, as well as host cell glycoconjugates might disrupt critical physiological events, such as the building of effective immune responses. This review aims to discuss the importance of mucin-like glycoproteins and both aTS and iTS for T. cruzi biology, as well as to present a snapshot of how disturbances in both parasite and host cell sialoglycophenotypes may facilitate the persistence of T. cruzi in the infected mammalian host.
Collapse
Affiliation(s)
- Leonardo Marques da Fonseca
- Laboratório de Glicobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kelli Monteiro da Costa
- Laboratório de Glicobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victoria de Sousa Chaves
- Laboratório de Glicobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Célio Geraldo Freire-de-Lima
- Laboratório de Imunomodulação, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Morrot
- Laboratório de Pesquisa em Tuberculose, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Laboratório de Imunoparasitologia, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lucia Mendonça-Previato
- Laboratório de Glicobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jose Osvaldo Previato
- Laboratório de Glicobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Freire-de-Lima
- Laboratório de Glicobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
2
|
Cossio-Pérez R, Pierdominici-Sottile G, Sobrado P, Palma J. Molecular Dynamics Simulations of Substrate Release from Trypanosoma cruzi UDP-Galactopyranose Mutase. J Chem Inf Model 2019; 59:809-817. [PMID: 30608160 DOI: 10.1021/acs.jcim.8b00675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The enzyme UDP-galactopyranose mutase (UGM) represents a promising drug target for the treatment of infections with Trypanosoma cruzi. We have computed the Potential of Mean Force for the release of UDP-galactopyranose from UGM, using Umbrella Sampling simulations. The simulations revealed the conformational changes that both substrate and enzyme undergo during the process. It was determined that the galactopyranose portion of the substrate is highly mobile and that the opening/closing of the active site occurs in stages. Previously uncharacterized interactions with highly conserved residues were also identified. These findings provide new pieces of information that contribute to the rational design of drugs against T. cruzi.
Collapse
Affiliation(s)
- Rodrigo Cossio-Pérez
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
| | - Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
| | - Pablo Sobrado
- Department of Biochemistry , Virginia Tech , Blacksburg , Virginia 24060 , United States
| | - Juliana Palma
- Departamento de Ciencia y Tecnología , Universidad Nacional de Quilmes , CONICET, Bernal , Buenos Aires B1876BXD , Argentina
| |
Collapse
|
3
|
Gadda G, Sobrado P. Kinetic Solvent Viscosity Effects as Probes for Studying the Mechanisms of Enzyme Action. Biochemistry 2018; 57:3445-3453. [DOI: 10.1021/acs.biochem.8b00232] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| |
Collapse
|
4
|
Sobrado P, Tanner JJ. Multiple functionalities of reduced flavin in the non-redox reaction catalyzed by UDP-galactopyranose mutase. Arch Biochem Biophys 2017; 632:59-65. [PMID: 28652025 DOI: 10.1016/j.abb.2017.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 12/29/2022]
Abstract
Flavin cofactors are widely used by enzymes to catalyze a broad range of chemical reactions. Traditionally, flavins in enzymes are regarded as redox centers, which enable enzymes to catalyze the oxidation or reduction of substrates. However, a new class of flavoenzyme has emerged over the past quarter century in which the flavin functions as a catalytic center in a non-redox reaction. Here we introduce the unifying concept of flavin hot spots to understand and categorize the mechanisms and reactivities of both traditional and noncanonical flavoenzymes. The major hot spots of reactivity include the N5, C4a, and C4O atoms of the isoalloxazine, and the 2' hydroxyl of the ribityl chain. The role of hot spots in traditional flavoenzymes, such as monooxygenases, is briefly reviewed. A more detailed description of flavin hot spots in noncanonical flavoenzymes is provided, with a focus on UDP-galactopyranose mutase, where the N5 functions as a nucleophile that attacks the anomeric carbon atom of the substrate. Recent results from mechanistic enzymology, kinetic crystallography, and computational chemistry provide a complete picture of the chemical mechanism of UDP-galactopyranose mutase.
Collapse
Affiliation(s)
- Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
| | - John J Tanner
- Departments of Biochemistry and Chemistry, University of Missouri, Columbia, MO 65211, USA.
| |
Collapse
|
5
|
Cossio-Pérez R, Palma J, Pierdominici-Sottile G. Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins. J Chem Inf Model 2017; 57:826-834. [PMID: 28301154 DOI: 10.1021/acs.jcim.6b00646] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.
Collapse
Affiliation(s)
- Rodrigo Cossio-Pérez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina
| | - Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, B1876BXD Bernal, Argentina
| |
Collapse
|
6
|
Misra S, Valicherla GR, Mohd Shahab, Gupta J, Gayen JR, Misra-Bhattacharya S. UDP-galactopyranose mutase, a potential drug target against human pathogenic nematodeBrugia malayi. Pathog Dis 2016; 74:ftw072. [DOI: 10.1093/femspd/ftw072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 01/02/2023] Open
|
7
|
Da Fonseca I, Qureshi IA, Mehra-Chaudhary R, Kizjakina K, Tanner JJ, Sobrado P. Contributions of unique active site residues of eukaryotic UDP-galactopyranose mutases to substrate recognition and active site dynamics. Biochemistry 2014; 53:7794-804. [PMID: 25412209 PMCID: PMC4270374 DOI: 10.1021/bi501008z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
UDP-galactopyranose mutase (UGM)
catalyzes the interconversion
between UDP-galactopyranose and UDP-galactofuranose. Absent in humans,
galactofuranose is found in bacterial and fungal cell walls and is
a cell surface virulence factor in protozoan parasites. For these
reasons, UGMs are targets for drug discovery. Here, we report a mutagenesis
and structural study of the UGMs from Aspergillus fumigatus and Trypanosoma cruzi focused on
active site residues that are conserved in eukaryotic UGMs but are
absent or different in bacterial UGMs. Kinetic analysis of the variants
F66A, Y104A, Q107A, N207A, and Y317A (A. fumigatus numbering) show decreases in kcat/KM values of 200–1000-fold for the mutase
reaction. In contrast, none of the mutations significantly affect
the kinetics of enzyme activation by NADPH. These results indicate
that the targeted residues are important for promoting the transition
state conformation for UDP-galactofuranose formation. Crystal structures
of the A. fumigatus mutant enzymes
were determined in the presence and absence of UDP to understand the
structural consequences of the mutations. The structures suggest important
roles for Asn207 in stabilizing the closed active site, and Tyr317
in positioning of the uridine ring. Phe66 and the corresponding residue
in Mycobacterium tuberculosis UGM (His68)
play a role as the backstop, stabilizing the galactopyranose group
for nucleophilic attack. Together, these results provide insight into
the essentiality of the targeted residues for realizing maximal catalytic
activity and a proposal for how conformational changes that close
the active site are temporally related and coupled together.
Collapse
Affiliation(s)
- Isabel Da Fonseca
- Department of Biochemistry, Virginia Tech , Blacksburg, Virginia 24061, United States
| | | | | | | | | | | |
Collapse
|
8
|
Pierdominici-Sottile G, Cossio Pérez R, Galindo JF, Palma J. QM/MM molecular dynamics study of the galactopyranose → galactofuranose reaction catalysed by Trypanosoma cruzi UDP-galactopyranose mutase. PLoS One 2014; 9:e109559. [PMID: 25299056 PMCID: PMC4192007 DOI: 10.1371/journal.pone.0109559] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/25/2014] [Indexed: 12/18/2022] Open
Abstract
The enzyme UDP-Galactopyranose Mutase (UGM) catalyses the conversion of galactopyranose into galactofuranose. It is known to be critical for the survival and proliferation of several pathogenic agents, both prokaryotic and eukaryotic. Among them is Trypanosoma cruzi, the parasite responsible for Chagas' disease. Since the enzyme is not present in mammals, it appears as a promising target for the design of drugs to treat this illness. A precise knowledge of the mechanism of the catalysed reaction would be crucial to assist in such design. In this article we present a detailed study of all the putative steps of the mechanism. The study is based on QM/MM free energy calculations along properly selected reaction coordinates, and on the analysis of the main structural changes and interactions taking place at every step. The results are discussed in connection with the experimental evidence and previous theoretical studies.
Collapse
Affiliation(s)
| | - Rodrigo Cossio Pérez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Johan F. Galindo
- Quantum and Computational Chemistry Group, Departamento de Química, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| |
Collapse
|
9
|
Durrant JD, Votapka L, Sørensen J, Amaro RE. POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. J Chem Theory Comput 2014; 10:5047-5056. [PMID: 25400521 PMCID: PMC4230373 DOI: 10.1021/ct500381c] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Indexed: 02/08/2023]
Abstract
![]()
Analysis of macromolecular/small-molecule
binding pockets can provide
important insights into molecular recognition and receptor dynamics.
Since its release in 2011, the POVME (POcket Volume MEasurer) algorithm
has been widely adopted as a simple-to-use tool for measuring and
characterizing pocket volumes and shapes. We here present POVME 2.0,
which is an order of magnitude faster, has improved accuracy, includes
a graphical user interface, and can produce volumetric density maps
for improved pocket analysis. To demonstrate the utility of the algorithm,
we use it to analyze the binding pocket of RNA editing ligase 1 from
the unicellular parasite Trypanosoma brucei, the
etiological agent of African sleeping sickness. The POVME analysis
characterizes the full dynamics of a potentially druggable transient
binding pocket and so may guide future antitrypanosomal drug-discovery
efforts. We are hopeful that this new version will be a useful tool
for the computational- and medicinal-chemist community.
Collapse
Affiliation(s)
- Jacob D Durrant
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States ; National Biomedical Computation Resource, Center for Research in Biological Systems, University of California San Diego , La Jolla, California 92093, United States
| | - Lane Votapka
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States
| | - Jesper Sørensen
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry, University of California San Diego , La Jolla, California 92093, United States ; National Biomedical Computation Resource, Center for Research in Biological Systems, University of California San Diego , La Jolla, California 92093, United States
| |
Collapse
|
10
|
Boechi L, Pierce L, Komives EA, McCammon JA. Trypsinogen activation as observed in accelerated molecular dynamics simulations. Protein Sci 2014; 23:1550-8. [PMID: 25131668 DOI: 10.1002/pro.2532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 06/17/2014] [Accepted: 08/03/2014] [Indexed: 11/07/2022]
Abstract
Serine proteases are involved in many fundamental physiological processes, and control of their activity mainly results from the fact that they are synthetized in an inactive form that becomes active upon cleavage. Three decades ago Martin Karplus's group performed the first molecular dynamics simulations of trypsin, the most studied member of the serine protease family, to address the transition from the zymogen to its active form. Based on the computational power available at the time, only high frequency fluctuations, but not the transition steps, could be observed. By performing accelerated molecular dynamics (aMD) simulations, an interesting approach that increases the configurational sampling of atomistic simulations, we were able to observe the N-terminal tail insertion, a crucial step of the transition mechanism. Our results also support the hypothesis that the hydrophobic effect is the main force guiding the insertion step, although substantial enthalpic contributions are important in the activation mechanism. As the N-terminal tail insertion is a conserved step in the activation of serine proteases, these results afford new perspective on the underlying thermodynamics of the transition from the zymogen to the active enzyme.
Collapse
Affiliation(s)
- Leonardo Boechi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | | | | | | |
Collapse
|
11
|
Tanner JJ, Boechi L, Andrew McCammon J, Sobrado P. Structure, mechanism, and dynamics of UDP-galactopyranose mutase. Arch Biochem Biophys 2014; 544:128-41. [PMID: 24096172 PMCID: PMC3946560 DOI: 10.1016/j.abb.2013.09.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 09/25/2013] [Accepted: 09/26/2013] [Indexed: 11/16/2022]
Abstract
The flavoenzyme UDP-galactopyranose mutase (UGM) is a key enzyme in galactofuranose biosynthesis. The enzyme catalyzes the 6-to-5 ring contraction of UDP-galactopyranose to UDP-galactofuranose. Galactofuranose is absent in humans yet is an essential component of bacterial and fungal cell walls and a cell surface virulence factor in protozoan parasites. Thus, inhibition of galactofuranose biosynthesis is a valid strategy for developing new antimicrobials. UGM is an excellent target in this effort because the product of the UGM reaction represents the first appearance of galactofuranose in the biosynthetic pathway. The UGM reaction is redox neutral, which is atypical for flavoenzymes, motivating intense examination of the chemical mechanism and structural features that tune the flavin for its unique role in catalysis. These studies show that the flavin functions as nucleophile, forming a flavin-sugar adduct that facilitates galactose-ring opening and contraction. The 3-dimensional fold is novel and conserved among all UGMs, however the larger eukaryotic enzymes have additional secondary structure elements that lead to significant differences in quaternary structure, substrate conformation, and conformational flexibility. Here we present a comprehensive review of UGM three-dimensional structure, provide an update on recent developments in understanding the mechanism of the enzyme, and summarize computational studies of active site flexibility.
Collapse
Affiliation(s)
- John J Tanner
- Departments of Chemistry and Biochemistry, University of Missouri, Columbia, MO, United States.
| | - Leonardo Boechi
- Departments of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States
| | - J Andrew McCammon
- Departments of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States; Howard Hughes Medical Institute, Department of Pharmacology, University of California San Diego, La Jolla, CA, United States
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States; Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States.
| |
Collapse
|