Publications by authors named "Mauricio Carrillo-Tripp"

22 Publications

  • Page 1 of 1

NAT2 polymorphisms associated with the development of hepatotoxicity after first-line tuberculosis treatment in Mexican patients: From genotype to molecular structure characterization.

Clin Chim Acta 2021 Apr 29;519:153-162. Epub 2021 Apr 29.

Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Calle 2 de abril - Jesús Dionisio González, Independencia, C.P. 64720 Monterrey, Nuevo León, Mexico. Electronic address:

Background And Aims: To assess the relevance of the slow acetylator phenotype based on NAT2 genotypes, among patients with pulmonary tuberculosis (PTB) that developed hepatotoxicity after first-line tuberculosis treatment in a Northeastern Mexican population.

Methods: Ninety one PTB patients were included, 7 of them developed hepatotoxicity. NAT2 SNPs (rs1801279, rs1041983, rs1801280, rs1799929, rs1799930, rs1208, and rs1799931) were genotyped by TaqMan allelic discrimination assay. Statistical analyses were performed using Epi Info statistical software 7.0 and SHEsisPlus for haplotype reconstruction. The NAT2 slow non-synonymous SNP were studied by molecular dynamic analysis (MDA).

Results: The frequency of the haplotype associated with slow acetylation status for PTB was 58%, and for with hepatotoxicity (PTB-H) represented 42.6%. Three haplotypes, NAT2*5Q, NAT2*5U, NAT2*5Va were exclusively present in seven PTB-H patients, (P = 0.01, P = 0.0006, P = 0.01, respectively). These haplotypes include the combination of two SNPs (I114T + R197Q or I114T + G286E). The effect of the SNPs on protein structure is to disrupt the CoA binding site affecting acetylation activity.

Conclusion: Our study provides insight into slow acetylation NAT2 haplotypes associated with hepatotoxicity after first-line tuberculosis treatment, for first time, in a Mexican population. The molecular mechanism acts at the CoA binding site.
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http://dx.doi.org/10.1016/j.cca.2021.04.017DOI Listing
April 2021

VIPERdb v3.0: a structure-based data analytics platform for viral capsids.

Nucleic Acids Res 2021 01;49(D1):D809-D816

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

VIrus Particle ExploreR data base (VIPERdb) (http://viperdb.scripps.edu) is a curated repository of virus capsid structures and a database of structure-derived data along with various virus specific information. VIPERdb has been continuously improved for over 20 years and contains a number of virus structure analysis tools. The release of VIPERdb v3.0 contains new structure-based data analytics tools like Multiple Structure-based and Sequence Alignment (MSSA) to identify hot-spot residues within a selected group of structures and an anomaly detection application to analyze and curate the structure-derived data within individual virus families. At the time of this writing, there are 931 virus structures from 62 different virus families in the database. Significantly, the new release also contains a standalone database called 'Virus World database' (VWdb) that comprises all the characterized viruses (∼181 000) known to date, gathered from ICTVdb and NCBI, and their capsid protein sequences, organized according to their virus taxonomy with links to known structures in VIPERdb and PDB. Moreover, the new release of VIPERdb includes a service-oriented data engine to handle all the data access requests and provides an interface for futuristic data analytics using machine leaning applications.
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http://dx.doi.org/10.1093/nar/gkaa1096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779063PMC
January 2021

Analyzing structural alterations of mitochondrial intermembrane space superoxide scavengers cytochrome-c and SOD1 after methylglyoxal treatment.

PLoS One 2020 30;15(4):e0232408. Epub 2020 Apr 30.

Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional Unidad Monterrey, Parque PIIT, Apodaca, Nuevo León, México.

Mitochondria are quantitatively the most important sources of reactive oxygen species (ROS) which are formed as by-products during cellular respiration. ROS generation occurs when single electrons are transferred to molecular oxygen. This leads to a number of different ROS types, among them superoxide. Although most studies focus on ROS generation in the mitochondrial matrix, the intermembrane space (IMS) is also important in this regard. The main scavengers for the detoxification of superoxide in the IMS are Cu, Zn superoxide dismutase (SOD1) and cytochrome-c. Similar to ROS, certain reactive carbonyl species are known for their high reactivity. The consequences are deleterious modifications to essential components compromising cellular functions and contributing to the etiology of severe pathological conditions like cancer, diabetes and neurodegeneration. In this study, we investigated the susceptibility of SOD1 and cytochrome-c to in vitro glycation by the dicarbonyl methylglyoxal (MGO) and the resulting effects on their structure. We utilized experimental techniques like immunodetection of the MGO-mediated modification 5-hydro-5-methylimidazolone, differential scanning calorimetry, fluorescence emission and circular dichroism measurements. We found that glycation of cytochrome-c leads to monomer aggregation, an altered secondary structure (increase in alpha helical content) and slightly more compact folding. In addition to structural changes, glycated cytochrome-c displays an altered thermal unfolding behavior. Subjecting SOD1 to MGO does not influence its secondary structure. However, similar to cytochrome-c, subunit aggregation is observed under denaturating conditions. Furthermore, the appearance of a second peak in the calorimetry diagram indirectly suggests de-metallation of SOD1 when high MGO levels are used. In conclusion, our data demonstrate that MGO has the potential to alter several structural parameters in important proteins of energy metabolism (cytochrome-c) and antioxidant defense (cytochrome-c, SOD1).
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232408PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7192434PMC
July 2020

Hot Spots and Their Contribution to the Self-Assembly of the Viral Capsid: In Silico Prediction and Analysis.

Int J Mol Sci 2019 Nov 27;20(23). Epub 2019 Nov 27.

Biomolecular Diversity Laboratory, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, C.P. 66600 Apodaca, Nuevo León, Mexico.

The viral capsid is a macromolecular complex formed by a defined number of self-assembled proteins, which, in many cases, are biopolymers with an identical amino acid sequence. Specific protein-protein interactions (PPI) drive the capsid self-assembly process, leading to several distinct protein interfaces. Following the PPI hot spot hypothesis, we present a conservation-based methodology to identify those interface residues hypothesized to be crucial elements on the self-assembly and thermodynamic stability of the capsid. We validate the predictions through a rigorous physical framework which integrates molecular dynamics simulations and free energy calculations by Umbrella sampling and the potential of mean force using an all-atom molecular representation of the capsid proteins of an icosahedral virus in an explicit solvent. Our results show that a single mutation in any of the structure-conserved hot spots significantly perturbs the quaternary protein-protein interaction, decreasing the absolute value of the binding free energy, without altering the protein's secondary nor tertiary structure. Our conservation-based hot spot prediction methodology can lead to strategies to rationally modulate the capsid's thermodynamic properties.
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http://dx.doi.org/10.3390/ijms20235966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6928768PMC
November 2019

VIPERdb: A Tool for Virus Research.

Annu Rev Virol 2018 09;5(1):477-488

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA; email:

The VIrus Particle ExploreR database (VIPERdb) ( http://viperdb.scripps.edu ) is a database and web portal for primarily icosahedral virus capsid structures that integrates structure-derived information with visualization and analysis tools accessed through a set of web interfaces. Our aim in developing VIPERdb is to provide comprehensive structure-derived information on viruses comprising simple to detailed attributes such as size (diameter), architecture ( T number), genome type, taxonomy, intersubunit association energies, and surface-accessible residues. In addition, a number of web-based tools are provided to enable users to interact with the structures and compare and contrast structure-derived properties between different viruses. Recently, we have constructed a series of data visualizations using modern JavaScript charting libraries such as Google Charts that allow users to explore trends and gain insights based on the various data available in the database. Furthermore, we now include helical viruses and nonicosahedral capsids by implementing modified procedures for data curation and analysis. This article provides an up-to-date overview of VIPERdb, describing various data and tools that are currently available and how to use them to facilitate structure-based bioinformatics analysis of virus capsids.
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http://dx.doi.org/10.1146/annurev-virology-092917-043405DOI Listing
September 2018

HTMoL: full-stack solution for remote access, visualization, and analysis of molecular dynamics trajectory data.

J Comput Aided Mol Des 2018 08 6;32(8):869-876. Epub 2018 Aug 6.

Departamento de Computación, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México.

Research on biology has seen significant advances with the use of molecular dynamics (MD) simulations. The MD methodology enables explanation and discovery of molecular mechanisms in a wide range of natural processes and biological systems. The need to readily share the ever-increasing amount of MD data has been hindered by the lack of specialized bioinformatic tools. The difficulty lies in the efficient management of the data, i.e., in sending and processing 3D information for its visualization. In this work, we present HTMoL, a plug-in-free, secure GPU-accelerated web application specifically designed to stream and visualize MD trajectory data on a web browser. Now, individual research labs can publish MD data on the Internet, or use HTMoL to profoundly improve scientific reports by including supplemental MD data in a journal publication. HTMoL can also be used as a visualization interface to access MD trajectories generated on a high-performance computer center directly. Furthermore, the HTMoL architecture can be leveraged with educational efforts to improve learning in the fields of biology, chemistry, and physics.
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http://dx.doi.org/10.1007/s10822-018-0141-yDOI Listing
August 2018

CapsidMesh: Atomic-detail structured mesh representation of icosahedral viral capsids and the study of their mechanical properties.

Int J Numer Method Biomed Eng 2018 07 22;34(7):e2991. Epub 2018 Apr 22.

Laboratorio de la Diversidad Biomolecular, Centro de Investigación y de Estudios Avanzados Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT,, C.P. 66600, Apodaca, Nuevo León, México.

Viruses are the most abundant pathogens affecting all forms of life. A major component of a virus is a protein shell, known as the viral capsid, that encapsulates the genomic material. The fundamental functions of the capsid are to protect and transport the viral genome and recognize the host cell. Descriptions of this macromolecular complex have been proposed at different scales of approximation. Here, we introduce a methodology to generate a structured volumetric mesh of icosahedral viral capsids (CapsidMesh) based on the atomic positions of their constituents. Material properties of the capsid proteins can be set on every mesh element individually. Hence, we have control over all levels of protein structure (atoms, amino acids, subunits, oligomers, and capsid). The CapsidMesh models are suitable for numerical simulations and analysis of a physical process using a third-party package. In particular, we used our methodology to generate a CapsidMesh of several capsids previously characterized by atomic force microscopy experiments and then simulated the mechanical nanoindentation through the finite element method. By fitting to the experimental linear elastic response, we estimated the elastic modulus and mechanical stresses produced on the capsids. Our results show that the atomic detail of the CapsidMesh is sufficient to reproduce anisotropic properties of the particle.
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http://dx.doi.org/10.1002/cnm.2991DOI Listing
July 2018

Evolution of substrate specificity in a retained enzyme driven by gene loss.

Elife 2017 03 31;6. Epub 2017 Mar 31.

Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Mexico.

The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or gene, at which these pathways converge, appears to coevolve with the occurrence of and genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes.
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http://dx.doi.org/10.7554/eLife.22679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404923PMC
March 2017

An Amphotericin B Derivative Equally Potent to Amphotericin B and with Increased Safety.

PLoS One 2016;11(9):e0162171. Epub 2016 Sep 28.

Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Apartado Postal 48-3, 62251, Cuernavaca, Morelos, México.

Amphotericin B is the most potent antimycotic known to date. However due to its large collateral toxicity, its use, although long standing, had been limited. Many attempts have been made to produce derivatives with reduced collateral damage. The molecular mechanism of polyene has also been closely studied for this purpose and understanding it would contribute to the development of safe derivatives. Our study examined polyene action, including chemical synthesis, electrophysiology, pharmacology, toxicology and molecular dynamics. The results were used to support a novel Amphotericin B derivative with increased selectivity: L-histidine methyl ester of Amphotericin B. We found that this derivative has the same form of action as Amphotericin B, i.e. pore formation in the cell membrane. Its reduced dimerization in solution, when compared to Amphotericin B, is at least partially responsible for its increased selectivity. Here we also present the results of preclinical tests, which show that the derivative is just as potent as Amphotericin B and has increased safety.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162171PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5040443PMC
September 2016

Structure based sequence analysis of viral and cellular protein assemblies.

J Struct Biol 2016 12 29;196(3):299-308. Epub 2016 Jul 29.

Biomolecular Diversity Laboratory, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Mexico. Electronic address:

It is well accepted that, in general, protein structural similarity is strongly related to the amino acid sequence identity. To analyze in great detail the correlation, distribution and variation levels of conserved residues in the protein structure, we analyzed all available high-resolution structural data of 5245 cellular complex-forming proteins and 293 spherical virus capsid proteins (VCPs). We categorized and compare them in terms of protein structural regions. In all cases, the buried core residues are the most conserved, followed by the residues at the protein-protein interfaces. The solvent-exposed surface shows greater sequence variations. Our results provide evidence that cellular monomers and VCPs could be two extremes in the quaternary structural space, with cellular dimers and oligomers in between. Moreover, based on statistical analysis, we detected a distinct group of icosahedral virus families whose capsid proteins seem to evolve much slower than the rest of the protein complexes analyzed in this work.
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http://dx.doi.org/10.1016/j.jsb.2016.07.013DOI Listing
December 2016

Porcine circovirus type 2 protective epitope densely carried by chimeric papaya ringspot virus-like particles expressed in Escherichia coli as a cost-effective vaccine manufacture alternative.

Biotechnol Appl Biochem 2017 May 20;64(3):406-414. Epub 2016 Apr 20.

Unidad de Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Normalistas 800, Colinas de la Normal, Guadalajara, Jalisco 44270, México.

Porcine circovirus type 2 (PCV2) still represents a major problem to the swine industry worldwide, causing high mortality rates in infected animals. Virus-like particles (VLPs) have gained attention for vaccine development, serving both as scaffolds for epitope expression and immune response enhancers. The commercial subunit vaccines against PCV2 consist of VLPs formed by the self-assembly of PCV2 capsid protein (CP) expressed in the baculovirus vector system. In this work, a PCV2 protective epitope was inserted into three different regions of papaya ringspot virus (PRSV) CP, namely, the N- and C-termini and a predicted antigenic region located near the N-terminus. Wild-type and chimeric CPs were modeled in silico, expressed in Escherichia coli, purified, and visualized by transmission electron microscopy. This is the first report that shows the formation of chimeric VLPs using PRSV as epitope-presentation scaffold. Moreover, it was found that PCV2 epitope localization strongly influences VLP length. Also, the estimated yields of the chimeric VLPs at a small-scale level ranged between 65 and 80 mg/L of culture medium. Finally, the three chimeric VLPs induced high levels of immunoglobulin G against the PCV2 epitope in immunized BALB/c mice, suggesting that these chimeric VLPs can be used for swine immunoprophylaxis against PCV2.
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http://dx.doi.org/10.1002/bab.1491DOI Listing
May 2017

Antagonism or synergism between papaya ringspot virus and papaya mosaic virus in Carica papaya is determined by their order of infection.

Virology 2016 Feb 5;489:179-91. Epub 2016 Jan 5.

Departamento de Ingeniería Genética, Unidad Irapuato. Electronic address:

Antagonism between unrelated plant viruses has not been thoroughly described. Our studies show that two unrelated viruses, papaya ringspot virus (PRSV) and papaya mosaic virus (PapMV) produce different symptomatic outcomes during mixed infection depending on the inoculation order. Synergism occurs in plants infected first with PRSV or in plants infected simultaneously with PRSV and PapMV, and antagonism occurs in plants infected first with PapMV and later inoculated with PRSV. During antagonism, elevated pathogenesis-related (PR-1) gene expression and increased reactive oxygen species production indicated the establishment of a host defense resulting in the reduction in PRSV titers. Polyribosomal fractioning showed that PRSV affects translation of cellular eEF1α, PR-1, β-tubulin, and PapMV RNAs in planta, suggesting that its infection could be related to an imbalance in the translation machinery. Our data suggest that primary PapMV infection activates a defense response against PRSV and establishes a protective relationship with the papaya host.
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http://dx.doi.org/10.1016/j.virol.2015.11.026DOI Listing
February 2016

Highly efficient strategy for the heterologous expression and purification of soluble Cowpea chlorotic mottle virus capsid protein and in vitro pH-dependent assembly of virus-like particles.

J Virol Methods 2015 Dec 2;225:23-9. Epub 2015 Sep 2.

Biomolecular Diversity Laboratory, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Mexico. Electronic address:

Obtaining pure and soluble viral capsid proteins (CPs) has been a major challenge in the fields of science and technology in recent decades. In many cases, the CPs can self-assemble in the absence of a viral genome, resulting in non-infectious, empty virus-like particles (VLPs) which can be safely handled. The use of VLPs has found great potential in biotechnology and health purposes. In addition, VLPs are a good model system to study protein-protein interactions at the molecular level. In this work, an optimized strategy for the heterologous expression of the Cowpea chlorotic mottle virus (CCMV) CP based in Escherichia coli is described. The method is efficient, inexpensive and it consistently produces higher yields and greater purity levels than those reported so far. Additionally, one of the main advantages of this method is the prevention of the formation of inclusion bodies, thus allowing to directly obtain high amounts of the CP in a soluble and functionally active state with the capacity to readily form VLPs in vitro. The CCMV CP self-assembly pH dependence was also investigated, providing guidelines to easily modulate the process.
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http://dx.doi.org/10.1016/j.jviromet.2015.08.023DOI Listing
December 2015

Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)₈ isomerase evolutionary intermediates from a diverse metagenome.

BMC Evol Biol 2015 Jun 10;15:107. Epub 2015 Jun 10.

Evolution of Metabolic Diversity, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Norte, Carretera Irapuato - León, CP 36821, Irapuato, México.

Background: Current sequence-based approaches to identify enzyme functional shifts, such as enzyme promiscuity, have proven to be highly dependent on a priori functional knowledge, hampering our ability to reconstruct evolutionary history behind these mechanisms. Hidden Markov Model (HMM) profiles, broadly used to classify enzyme families, can be useful to distinguish between closely related enzyme families with different specificities. The (βα)8-isomerase HisA/PriA enzyme family, involved in L-histidine (HisA, mono-substrate) biosynthesis in most bacteria and plants, but also in L-tryptophan (HisA/TrpF or PriA, dual-substrate) biosynthesis in most Actinobacteria, has been used as model system to explore evolutionary hypotheses and therefore has a considerable amount of evolutionary, functional and structural knowledge available. We searched for functional evolutionary intermediates between the HisA and PriA enzyme families in order to understand the functional divergence between these families.

Results: We constructed a HMM profile that correctly classifies sequences of unknown function into the HisA and PriA enzyme sub-families. Using this HMM profile, we mined a large metagenome to identify plausible evolutionary intermediate sequences between HisA and PriA. These sequences were used to perform phylogenetic reconstructions and to identify functionally conserved amino acids. Biochemical characterization of one selected enzyme (CAM1) with a mutation within the functionally essential N-terminus phosphate-binding site, namely, an alanine instead of a glycine in HisA or a serine in PriA, showed that this evolutionary intermediate has dual-substrate specificity. Moreover, site-directed mutagenesis of this alanine residue, either backwards into a glycine or forward into a serine, revealed the robustness of this enzyme. None of these mutations, presumably upon functionally essential amino acids, significantly abolished its enzyme activities. A truncated version of this enzyme (CAM2) predicted to adopt a (βα)6-fold, and thus entirely lacking a C-terminus phosphate-binding site, was identified and shown to have HisA activity.

Conclusion: As expected, reconstruction of the evolution of PriA from HisA with HMM profiles suggest that functional shifts involve mutations in evolutionarily intermediate enzymes of otherwise functionally essential residues or motifs. These results are in agreement with a link between promiscuous enzymes and intragenic epistasis. HMM provides a convenient approach for gaining insights into these evolutionary processes.
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http://dx.doi.org/10.1186/s12862-015-0378-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4462073PMC
June 2015

CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps.

J Struct Biol 2015 Apr 16;190(1):47-55. Epub 2015 Feb 16.

Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.

Structural analysis and visualization of protein-protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces. In the case of viruses, structural analysis becomes even more demanding because several interfaces coexist and, in most cases, these are formed by hundreds of contacting residues that belong to multiple interacting coat proteins. CapsidMaps is an interactive analysis and visualization tool that is designed to benefit the structural virology community. Developed as an improved extension of the φ-ψ Explorer, here we describe the details of its design and implementation. We present results of analysis of a spherical virus to showcase the features and utility of the new tool. CapsidMaps also facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity (S)-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application at http://viperdb.scripps.edu.
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http://dx.doi.org/10.1016/j.jsb.2015.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750372PMC
April 2015

Evolution of substrate specificity in a recipient's enzyme following horizontal gene transfer.

Mol Biol Evol 2013 Sep 25;30(9):2024-34. Epub 2013 Jun 25.

Evolution of Metabolic Diversity Laboratory, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Cinvestav-IPN, Irapuato, México.

Despite the prominent role of horizontal gene transfer (HGT) in shaping bacterial metabolism, little is known about the impact of HGT on the evolution of enzyme function. Specifically, what is the influence of a recently acquired gene on the function of an existing gene? For example, certain members of the genus Corynebacterium have horizontally acquired a whole l-tryptophan biosynthetic operon, whereas in certain closely related actinobacteria, for example, Mycobacterium, the trpF gene is missing. In Mycobacterium, the function of the trpF gene is performed by a dual-substrate (βα)8 phosphoribosyl isomerase (priA gene) also involved in l-histidine (hisA gene) biosynthesis. We investigated the effect of a HGT-acquired TrpF enzyme upon PriA's substrate specificity in Corynebacterium through comparative genomics and phylogenetic reconstructions. After comprehensive in vivo and enzyme kinetic analyses of selected PriA homologs, a novel (βα)8 isomerase subfamily with a specialized function in l-histidine biosynthesis, termed subHisA, was confirmed. X-ray crystallography was used to reveal active-site mutations in subHisA important for narrowing of substrate specificity, which when mutated to the naturally occurring amino acid in PriA led to gain of function. Moreover, in silico molecular dynamic analyses demonstrated that the narrowing of substrate specificity of subHisA is concomitant with loss of ancestral protein conformational states. Our results show the importance of HGT in shaping enzyme evolution and metabolism.
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http://dx.doi.org/10.1093/molbev/mst115DOI Listing
September 2013

Immune response to a potyvirus with exposed amino groups available for chemical conjugation.

Virol J 2012 Mar 27;9:75. Epub 2012 Mar 27.

Unidad de Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Normalistas 800, Colinas de la Normal, Guadalajara, Jalisco 44270, México.

Background: The amino terminus of the tobacco etch virus (TEV) capsid protein is located on the external surface of infectious TEV particles, as proposed by previous studies and an in silico model. The epsilon amino groups on the exposed lysine residues are available for chemical conjugation to any given protein, and can thus act as antigen carriers. The availability of amino groups on the surfaces of TEV particles was determined and the immune response to TEV evaluated.

Results: Using a biotin-tagged molecule that reacts specifically with amino groups, we found that the TEV capsid protein has amino groups on its surface available for coupling to other molecules via crosslinkers. Intraperitoneal TEV was administered to female BALB/c mice, and both their humoral and cellular responses measured. Different IgG isotypes, particularly IgG2a, directed against TEV were induced. In a cell proliferation assay, only spleen cells from vaccinated mice that were stimulated in vitro with TEV showed significant proliferation of CD3+/CD4+ and CD3+/CD8+ subpopulations and secreted significant amounts of interferon γ.

Conclusions: TEV has surface amino groups that are available for chemical coupling. TEV induces both humoral and cellular responses when administered alone intraperitoneally to mice. Therefore, TEV should be evaluated as a vaccine adjuvant when chemically coupled to antigens of choice.
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http://dx.doi.org/10.1186/1743-422X-9-75DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3359163PMC
March 2012

VIPERdb2: an enhanced and web API enabled relational database for structural virology.

Nucleic Acids Res 2009 Jan 3;37(Database issue):D436-42. Epub 2008 Nov 3.

Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb(2), we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Phi-Psi (Phi-Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence-structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.
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http://dx.doi.org/10.1093/nar/gkn840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686430PMC
January 2009

A novel method to map and compare protein-protein interactions in spherical viral capsids.

Proteins 2008 Nov;73(3):644-55

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Viral capsids are composed of multiple copies of one or a few chemically distinct capsid proteins and are mostly stabilized by inter subunit protein-protein interactions. There have been efforts to identify and analyze these protein-protein interactions, in terms of their extent and similarity, between the subunit interfaces related by quasi- and icosahedral symmetry. Here, we describe a new method to map quaternary interactions in spherical virus capsids onto polar angle space with respect to the icosahedral symmetry axes using azimuthal orthographic diagrams. This approach enables one to map the nonredundant interactions in a spherical virus capsid, irrespective of its size or triangulation number (T), onto the reference icosahedral asymmetric unit space. The resultant diagrams represent characteristic fingerprints of quaternary interactions of the respective capsids. Hence, they can be used as road maps of the protein-protein interactions to visualize the distribution and the density of the interactions. In addition, unlike the previous studies, the fingerprints of different capsids, when represented in a matrix form, can be compared with one another to quantitatively evaluate the similarity (S-score) in the subunit environments and the associated protein-protein interactions. The S-score selectively distinguishes the similarity, or lack of it, in the locations of the quaternary interactions as opposed to other well-known structural similarity metrics (e.g., RMSD, TM-score). Application of this method on a subset of T = 1 and T = 3 capsids suggests that S-score values range between 1 and 0.6 for capsids that belong to the same virus family/genus; 0.6-0.3 for capsids from different families with the same T-number and similar subunit fold; and <0.3 for comparisons of the dissimilar capsids that display different quaternary architectures (T-numbers). Finally, the sequence conserved interface residues within a virus family, whose spatial locations were also conserved have been hypothesized as the essential residues for self-assembly of the member virus capsids.
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http://dx.doi.org/10.1002/prot.22088DOI Listing
November 2008

Ion hydration in nanopores and the molecular basis of selectivity.

Biophys Chem 2006 Dec 3;124(3):243-50. Epub 2006 May 3.

Chemistry Department, Wabash College, P.O. Box 352, Crawfordsville, IN 47933, USA.

Using a simple model, it is shown that the cost of constraining a hydrated potassium ion inside a narrow pore is smaller than the cost of constraining hydrated sodium or lithium ions in pores of radius around 1.5 A. The opposite is true for pores of radius around 2.5 A. The reason for the selectivity in the first region is that the potassium ion allows for a greater distortion of its hydration shell and can therefore maintain a better coordination, and the reason for the reverse selectivity in the second region is that the smaller ions retain their hydration shells in these pores. This is relevant to the molecular basis of ion selective channels, and since this mechanism does not depend on the molecular details of the pore, it could also operate in all sorts of nanotubes.
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http://dx.doi.org/10.1016/j.bpc.2006.04.012DOI Listing
December 2006

Evidence for a mechanism by which omega-3 polyunsaturated lipids may affect membrane protein function.

Biochemistry 2005 Aug;44(30):10164-9

Department of Chemistry, Wabash College, 301 West Wabash Avenue, Crawfordsville, Indiana 47933, USA.

We have calculated the lateral pressure profile from well-converged, experimentally validated, molecular dynamics simulations of hydrated lipid bilayer membranes containing highly polyunsaturated fatty acids. The three simulations, each 30 ns in length, contain omega-3 fatty acids, omega-6 fatty acids, and a mixture of omega-3 fatty acids and cholesterol and were continued from previously published simulations that demonstrated excellent agreement with a wide variety of experimental measurements. We find that the distribution of lateral stress within the hydrophobic core of the membrane is sensitively dependent on the degree of chain unsaturation and on the presence of cholesterol. Replacing omega-3 fatty acids with omega-6 chains, or incorporating cholesterol into the membrane, shifts the repulsive lateral chain pressure away from the lipid/water interface toward the bilayer interior. This may support a previously proposed mechanism by which lipid composition may affect conformational equilibrium for integral membrane proteins.
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http://dx.doi.org/10.1021/bi050822eDOI Listing
August 2005

Minimalist molecular model for nanopore selectivity.

Phys Rev Lett 2004 Oct 14;93(16):168104. Epub 2004 Oct 14.

Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, 62210 Cuernavaca, Morelos, México.

Using a simple model it is shown that the cost of constraining a hydrated potassium ion inside a narrow nanopore is smaller than the cost of constraining the smaller hydrated sodium ion. The former allows for a greater distortion of its hydration shell and can therefore maintain a better coordination. We propose that in this way the larger ion can go through narrow pores more easily. This is relevant to the molecular basis of ion selective nanopores and since this mechanism does not depend on the molecular details of the pore, it could also operate in all sorts of nanotubes, from biological to synthetic.
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http://dx.doi.org/10.1103/PhysRevLett.93.168104DOI Listing
October 2004