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1.
Biochem J ; 476(5): 809-826, 2019 03 12.
Artículo en Inglés | MEDLINE | ID: mdl-30782970

RESUMEN

SPH (self-incompatibility protein homologue) proteins are a large family of small, disulfide-bonded, secreted proteins, initially found in the self-incompatibility response in the field poppy (Papaver rhoeas), but now known to be widely distributed in plants, many containing multiple members of this protein family. Using the Origami strain of Escherichia coli, we expressed one member of this family, SPH15 from Arabidopsis thaliana, as a folded thioredoxin fusion protein and purified it from the cytosol. The fusion protein was cleaved and characterised by analytical ultracentrifugation, circular dichroism and nuclear magnetic resonance (NMR) spectroscopy. This showed that SPH15 is monomeric and temperature stable, with a ß-sandwich structure. The four strands in each sheet have the same topology as the unrelated proteins: human transthyretin, bacterial TssJ and pneumolysin, with no discernible sequence similarity. The NMR-derived structure was compared with a de novo model, made using a new deep learning algorithm based on co-evolution/correlated mutations, DeepCDPred, validating the method. The DeepCDPred de novo method and homology modelling to SPH15 were then both used to derive models of the 3D structure of the three known PrsS proteins from P. rhoeas, which have only 15-18% sequence homology to SPH15. The DeepCDPred method gave models with lower discreet optimised protein energy scores than the homology models. Three loops at one end of the poppy structures are postulated to interact with their respective pollen receptors to instigate programmed cell death in pollen tubes.


Asunto(s)
Proteínas de Arabidopsis/química , Arabidopsis/química , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Bacterias/química , Bacterias/genética , Bacterias/metabolismo , Humanos , Dominios Proteicos , Estructura Secundaria de Proteína
2.
Chembiochem ; 19(8): 836-841, 2018 04 16.
Artículo en Inglés | MEDLINE | ID: mdl-29363252

RESUMEN

The addition or removal of hydroxy groups modulates the activity of many pharmacologically active biomolecules. It can be integral to the basic biosynthetic factory or result from associated tailoring steps. For the anti-MRSA antibiotic mupirocin, removal of a C8-hydroxy group late in the biosynthetic pathway gives the active pseudomonic acid A. An extra hydroxylation, at C4, occurs in the related but more potent antibiotic thiomarinol A. We report here in vivo and in vitro studies that show that the putative non-haem-iron(II)/α-ketoglutaratedependent dioxygenase TmuB, from the thiomarinol cluster, 4-hydroxylates various pseudomonic acids whereas C8-OH, and other substituents around the tetrahydropyran ring, block enzyme action but not substrate binding. Molecular modelling suggested a basis for selectivity, but mutation studies had a limited ability to rationally modify TmuB substrate specificity. 4-Hydroxylation had opposite effects on the potency of mupirocin and thiomarinol. Thus, TmuB can be added to the toolbox of polyketide tailoring technologies for the in vivo generation of new antibiotics in the future.


Asunto(s)
Antibacterianos/farmacología , Oxigenasas de Función Mixta/antagonistas & inhibidores , Sintasas Poliquetidas/efectos de los fármacos , Antibacterianos/química , Hidroxilación , Sintasas Poliquetidas/metabolismo , Especificidad por Sustrato
3.
Angew Chem Int Ed Engl ; 56(14): 3930-3934, 2017 03 27.
Artículo en Inglés | MEDLINE | ID: mdl-28181382

RESUMEN

Thiomarinol and mupirocin are assembled on similar polyketide/fatty acid backbones and exhibit potent antibiotic activity against methicillin-resistant Staphylococcus aureus (MRSA). They both contain a tetrasubstituted tetrahydropyran (THP) ring that is essential for biological activity. Mupirocin is a mixture of pseudomonic acids (PAs). Isolation of the novel compound mupirocin P, which contains a 7-hydroxy-6-keto-substituted THP, from a ΔmupP strain and chemical complementation experiments confirm that the first step in the conversion of PA-B into the major product PA-A is oxidation at the C6 position. In addition, nine novel thiomarinol (TM) derivatives with different oxidation patterns decorating the central THP core were isolated after gene deletion (tmlF). These metabolites are in accord with the THP ring formation and elaboration in thiomarinol following a similar order to that found in mupirocin biosynthesis, despite the lack of some of the equivalent genes. Novel mupirocin-thiomarinol hybrids were also synthesized by mutasynthesis.


Asunto(s)
Antibacterianos/farmacología , Staphylococcus aureus Resistente a Meticilina/efectos de los fármacos , Mupirocina/análogos & derivados , Mupirocina/farmacología , Sintasas Poliquetidas/genética , Antibacterianos/química , Antibacterianos/metabolismo , Pruebas de Sensibilidad Microbiana , Conformación Molecular , Mupirocina/biosíntesis , Mupirocina/química , Mutación , Sintasas Poliquetidas/metabolismo
4.
Mol Microbiol ; 93(5): 911-27, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-24995530

RESUMEN

Laboratory-based evolution and whole-genome sequencing can link genotype and phenotype. We used evolution of acid resistance in exponential phase Escherichia coli to study resistance to a lethal stress. Iterative selection at pH 2.5 generated five populations that were resistant to low pH in early exponential phase. Genome sequencing revealed multiple mutations, but the only gene mutated in all strains was evgS, part of a two-component system that has already been implicated in acid resistance. All these mutations were in the cytoplasmic PAS domain of EvgS, and were shown to be solely responsible for the resistant phenotype, causing strong upregulation at neutral pH of genes normally induced by low pH. Resistance to pH 2.5 in these strains did not require the transporter GadC, or the sigma factor RpoS. We found that EvgS-dependent constitutive acid resistance to pH 2.5 was retained in the absence of the regulators GadE or YdeO, but was lost if the oxidoreductase YdeP was also absent. A deletion in the periplasmic domain of EvgS abolished the response to low pH, but not the activity of the constitutive mutants. On the basis of these results we propose a model for how EvgS may become activated by low pH.


Asunto(s)
Ácidos/metabolismo , Proteínas de Escherichia coli/genética , Escherichia coli/enzimología , Evolución Molecular , Proteínas Quinasas/genética , Secuencia de Aminoácidos , Escherichia coli/química , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Concentración de Iones de Hidrógeno , Modelos Moleculares , Datos de Secuencia Molecular , Mutación , Proteínas Quinasas/química , Proteínas Quinasas/metabolismo , Estructura Terciaria de Proteína
5.
Nat Chem Biol ; 9(11): 685-692, 2013 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-24056399

RESUMEN

Type I polyketide synthases often use programmed ß-branching, via enzymes of a 'hydroxymethylglutaryl-CoA synthase (HCS) cassette', to incorporate various side chains at the second carbon from the terminal carboxylic acid of growing polyketide backbones. We identified a strong sequence motif in acyl carrier proteins (ACPs) where ß-branching is known to occur. Substituting ACPs confirmed a correlation of ACP type with ß-branching specificity. Although these ACPs often occur in tandem, NMR analysis of tandem ß-branching ACPs indicated no ACP-ACP synergistic effects and revealed that the conserved sequence motif forms an internal core rather than an exposed patch. Modeling and mutagenesis identified ACP helix III as a probable anchor point of the ACP-HCS complex whose position is determined by the core. Mutating the core affects ACP functionality, whereas ACP-HCS interface substitutions modulate system specificity. Our method for predicting ß-carbon branching expands the potential for engineering new polyketides and lays a basis for determining specificity rules.


Asunto(s)
Proteína Transportadora de Acilo/química , Proteína Transportadora de Acilo/metabolismo , Secuencia Conservada , Hidroximetilglutaril-CoA Sintasa/metabolismo , Policétidos/metabolismo , Proteína Transportadora de Acilo/genética , Secuencias de Aminoácidos , Modelos Moleculares , Conformación Molecular , Policétidos/química
6.
Planta ; 236(6): 1927-41, 2012 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-22945313

RESUMEN

ARABIDILLO proteins regulate multicellular root development in Arabidopsis thaliana. Conserved ARABIDILLO homologues are present throughout land plants, even in early-evolving plants that do not possess complex root architecture, suggesting that ARABIDILLO genes have additional functions. Here, we have cloned and characterised ARABIDILLO gene homologues from two early-evolving land plants, the bryophyte Physcomitrella patens and the lycophyte Selaginella moellendorffii. We show that two of the PHYSCODILLO genes (PHYSCODILLO1A and -1B) exist as a tail-to-tail tandem array of two almost identical 12 kb sequences, while a third related gene (PHYSCODILLO2) is located elsewhere in the Physcomitrella genome. Physcomitrella possesses a very low percentage of tandemly arrayed genes compared with the later-evolving plants whose genomes have been sequenced to date. Thus, PHYSCODILLO1A and -1B genes represent a relatively unusual gene arrangement. PHYSCODILLO promoters are active largely in the haploid gametophyte, with additional activity at the foot of the sporophyte. The pattern of promoter activity is uniform in filamentous and leafy tissues, suggesting pleiotropic gene functions and likely functional redundancy: the latter possibility is confirmed by the lack of discernible phenotype in a physcodillo2 deletion mutant. Interestingly, the pattern of PHYSCODILLO promoter activity in female reproductive organs is strikingly similar to that of an Arabidopsis homologue, suggesting co-option of some PHYSCODILLO functions or regulation into both the sporophyte and gametophyte. In conclusion, our work identifies and characterises some of the earliest-evolving land plant ARABIDILLO homologues. We confirm that all land plant ARABIDILLO genes arose from a single common ancestor and suggest that PHYSCODILLO proteins have novel and pleiotropic functions, some of which may be conserved in later-evolving plants.


Asunto(s)
Bryopsida/genética , Genoma de Planta/genética , Proteínas de Plantas/genética , Selaginellaceae/genética , Arabidopsis/genética , Secuencia de Bases , Bryopsida/citología , Bryopsida/crecimiento & desarrollo , Regulación de la Expresión Génica de las Plantas , Genes Reporteros , Datos de Secuencia Molecular , Fenotipo , Filogenia , Plantas Modificadas Genéticamente , Regiones Promotoras Genéticas/genética , Selaginellaceae/citología , Selaginellaceae/crecimiento & desarrollo , Alineación de Secuencia , Análisis de Secuencia de ADN , Eliminación de Secuencia , Homología de Secuencia de Ácido Nucleico , Especificidad de la Especie
7.
Bioessays ; 31(12): 1357-66, 2009 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-19877003

RESUMEN

We present a molecular model of eukaryotic gene transcription. For the beta-globin locus, we hypothesise that a transcription machine composed of multiple RNA polymerase II (PolII) assembles using the locus control region as a foundation. Transcription and locus remodelling can be achieved by pulling DNA through this multi-PolII 'reading head'. Once a transcription complex is formed, it may engage an active gene in several rounds of transcription. Observed intergenic sense and antisense transcripts may be the result of PolII pulling the DNA through the reading head whilst searching for the promoter of a gene. Support for this hypothesis is provided using various data from the literature. In the model, DNA is packed in a 30-nm chromatin fibre, thus gene regulatory regions separated by kilobases are close in space. This, and the need to store transcription-induced supercoiling, may explain why functionally interacting regions are often separated by many kilobases.


Asunto(s)
Cromatina/genética , Desarrollo Embrionario/genética , Sitios Genéticos , Modelos Moleculares , ARN Polimerasa II/metabolismo , Transcripción Genética , Globinas beta/genética , Animales , Cromatina/metabolismo , Empaquetamiento del ADN/genética , Humanos
8.
J Phys Chem B ; 124(3): 461-469, 2020 01 23.
Artículo en Inglés | MEDLINE | ID: mdl-31859508

RESUMEN

Previously, we have demonstrated the effect of salt bridges on the electron capture dissociation mass spectrometry behavior of synthetic model phosphopeptides and applied an ion mobility spectrometry/molecular modeling approach to rationalize the findings in terms of peptide ion structure. Here, we develop and apply the approach to a biologically derived phosphopeptide. Specifically, we have investigated variants of a 15-mer phosphopeptide VVGARRSsWRVVSSI (s denotes phosphorylated Ser) derived from Akt1 substrate 14-3-3-ζ, which contains the phosphorylation motif RRSsWR. Variants were generated by successive arginine-to-leucine substitutions within the phosphorylation motif. ECD fragmentation patterns for the eight phosphopeptide variants show greater sequence coverage with successive R → L substitutions. Peptides with two or more basic residues had regions with no sequence coverage, while full sequence coverage was observed for peptides with one or no basic residues. For three of the peptide variants, low-abundance fragments were observed between the phosphoserine and a basic residue, possibly due to the presence of multiple conformers with and without noncovalent interactions between these residues. For the five variants whose dissociation behavior suggested the presence of intramolecular noncovalent interactions, we employed ion mobility spectrometry and molecular modeling to probe the nature of these interactions. Our workflow allowed us to propose candidate structures whose noncovalent interactions were consistent with the ECD data for all of the peptides modeled. Additionally, the AMBER parameter sets created for and validated by this work are presented and made available online ( http://www.biosciences-labs.bham.ac.uk/cooper/datasets.php ).


Asunto(s)
Proteínas 14-3-3/análisis , Fragmentos de Péptidos/análisis , Fosfopéptidos/análisis , Proteínas 14-3-3/química , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Espectrometría de Movilidad Iónica/métodos , Espectrometría de Masas/métodos , Modelos Moleculares , Fragmentos de Péptidos/química , Fosfopéptidos/química
9.
Sci Rep ; 9(1): 1542, 2019 02 07.
Artículo en Inglés | MEDLINE | ID: mdl-30733464

RESUMEN

The mupirocin trans-AT polyketide synthase pathway, provides a model system for manipulation of antibiotic biosynthesis. Its final phase involves removal of the tertiary hydroxyl group from pseudomonic acid B, PA-B, producing the fully active PA-A in a complex series of steps. To further clarify requirements for this conversion, we fed extracts containing PA-B to mutants of the producer strain singly deficient in each mup gene. This additionally identified mupM and mupN as required plus the sequence but not enzymic activity of mupL and ruled out need for other mup genes. A plasmid expressing mupLMNOPVCFU + macpE together with a derivative of the producer P. fluorescens strain NCIMB10586 lacking the mup cluster allowed conversion of PA-B to PA-A. MupN converts apo-mAcpE to holo-form while MupM is a mupirocin-resistant isoleucyl tRNA synthase, preventing self-poisoning. Surprisingly, the expression plasmid failed to allow the closely related P. fluorescens strain SBW25 to convert PA-B to PA-A.


Asunto(s)
Antibacterianos/metabolismo , Mupirocina/biosíntesis , Pseudomonas fluorescens/metabolismo , Antibacterianos/química , Bacillus subtilis/genética , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Escherichia coli/genética , Mupirocina/química , Mutagénesis , Plásmidos/genética , Plásmidos/metabolismo , Sintasas Poliquetidas/genética , Sintasas Poliquetidas/metabolismo , Policétidos/química , Policétidos/metabolismo , Pseudomonas fluorescens/genética
10.
Biochim Biophys Acta ; 1770(3): 390-401, 2007 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-16920266

RESUMEN

The active site of cytochromes P450 is situated deep inside the protein next to the heme cofactor. Consequently, enzyme specificity and kinetics can be influenced by how substrates pass through the protein to access the active site and how products egress from the active site. We previously analysed the channels between the active site and the protein surface in P450 crystal structures available in October 2003 [R.C. Wade, P.J. Winn, I. Schlichting, Sudarko, A survey of active site access channels in cytochromes P450, J. Inorg. Biochem. 98 (2004) 1175-1182]. Since then, 52 new P450 structures have been made available, including entries for ten isozymes for which structures were not previously available. We present an updated survey covering all P450 crystal structures available in March 2006. This survey shows channels not observed earlier in crystal structures, some of which were identified in previous molecular dynamics simulations. The crystal structures demonstrate how some of the channels can merge when the protein structure opens up resulting in a wide cleft to the active site, caused largely by movements of the F-G helix-loop-helix and the B-C loop. Significant differences were observed between the channels in the crystal structures of the mammalian and bacterial enzymes. The multiplicity of channels suggests possibilities for substrate channelling to and from the P450s.


Asunto(s)
Sistema Enzimático del Citocromo P-450/química , Modelos Moleculares , Pliegue de Proteína , Sitios de Unión , Conformación Proteica
11.
Proteins ; 71(4): 1955-69, 2008 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-18186463

RESUMEN

We present a computational procedure for modeling protein-protein association and predicting the structures of protein-protein complexes. The initial sampling stage is based on an efficient Brownian dynamics algorithm that mimics the physical process of diffusional association. Relevant biochemical data can be directly incorporated as distance constraints at this stage. The docked configurations are then grouped with a hierarchical clustering algorithm into ensembles that represent potential protein-protein encounter complexes. Flexible refinement of selected representative structures is done by molecular dynamics simulation. The protein-protein docking procedure was thoroughly tested on 10 structurally and functionally diverse protein-protein complexes. Starting from X-ray crystal structures of the unbound proteins, in 9 out of 10 cases it yields structures of protein-protein complexes close to those determined experimentally with the percentage of correct contacts >30% and interface backbone RMSD <4 A. Detailed examination of all the docking cases gives insights into important determinants of the performance of the computational approach in modeling protein-protein association and predicting of protein-protein complex structures.


Asunto(s)
Bioquímica , Simulación por Computador , Proteínas/química , Proteínas/metabolismo , Algoritmos , Secuencia de Aminoácidos , Animales , Fenómenos Bioquímicos , Biología Computacional/métodos , Cristalografía por Rayos X , Bases de Datos Factuales , Difusión , Análisis de Fourier , Humanos , Enlace de Hidrógeno , Modelos Biológicos , Datos de Secuencia Molecular , Concentración Osmolar , Conformación Proteica , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Electricidad Estática
12.
Front Biosci ; 12: 3419-30, 2007 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-17485310

RESUMEN

Post-translational modification by ubiquitin and ubiquitin-like (UBL) proteins is a key mechanism for cellular control. The specificity of the enzymes of ubiquitination and their close paralogs is dependent on their molecular electrostatic potentials. For example, analysis of molecular electrostatic potentials and electrostatically key residues can account for the selectivity of different E1s (activating enzymes) and of different SUMO proteases. The molecular interactions of the ubiquitin conjugating enzymes, the ubiquitin family proteins (UFP) and UBL domains are discussed in detail. An interesting observation is that the Non Canonical Ubiquitin Conjugating Enzymes (NCUBEs) have electrostatic potentials that are more similar to the UBC9 orthologs, the SUMO conjugating enzymes, than they are to other ubiquitin conjugating enzymes. It had previously been suggested that UBC9 may select for SUMO based on its difference in electrostatic potential as compared to other E2s but the NCUBE exception suggests that this may not be the case. The web site http://www.ubiquitin-resource.org/ allows users to find the E2s most electrostatically similar to a query E2. Where possible, models have been made for all E2 domains in the SMART database (http://smart.embl-heidelberg.de/). A brief overview of molecular electrostatic potentials and their application to understanding protein function is also given.


Asunto(s)
Electricidad Estática , Ubiquitina/metabolismo , Animales , Humanos , Conformación Proteica , Ubiquitina/fisiología
13.
Biochim Biophys Acta ; 1754(1-2): 239-44, 2005 Dec 30.
Artículo en Inglés | MEDLINE | ID: mdl-16226496

RESUMEN

Biomolecular recognition is complex. The balance between the different molecular properties that contribute to molecular recognition, such as shape, electrostatics, dynamics and entropy, varies from case to case. This, along with the extent of experimental characterization, influences the choice of appropriate computational approaches to study biomolecular interactions. Here, we present computational studies of cytochrome P450 enzymes and their interactions with small molecules and with other proteins. These interactions exemplify some of the diversity of molecular determinants of binding affinity and specificity observed for proteins and we discuss some of the challenges that they pose for molecular modelling and simulation.


Asunto(s)
Sistema Enzimático del Citocromo P-450/metabolismo , Modelos Moleculares , Sitios de Unión , Biología Computacional/métodos , Sistema Enzimático del Citocromo P-450/química , Ligandos , Modelos Químicos , Unión Proteica/efectos de los fármacos , Estructura Terciaria de Proteína , Proteínas/química , Proteínas/metabolismo , Relación Estructura-Actividad , Especificidad por Sustrato
14.
Structure ; 12(9): 1563-74, 2004 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-15341722

RESUMEN

The E2 enzymes are key enzymes in the ubiquitin and ubiquitin-like protein ligation pathways. To understand the functionality of the different E2 enzymes, we analyzed 190 protein sequences and 211 structures and electrostatic potentials. Key findings include: The ScUbc1 orthologs are defined by a C-terminal UBA domain. An N-terminal sequence motif that is highly conserved in all E2s except for Cdc34 orthologs is important for the stabilization of the L7 loop and is likely to be involved in E1 binding. ScUbc11p has a different electrostatic potential from E2-Cp and other proteins with which it has high sequence similarity but different functionality. All the E2s known to ubiquitinate histones have a negative potential. The members of the NCUBE family have a positive electrostatic potential, although its form is different from that of the SUMO conjugating E2s. The specificities of only the ScUbc4/Ubc5 and ScUbc1p orthologs are reflected in their L4 and L7 loops.


Asunto(s)
Estructura Terciaria de Proteína , Enzimas Ubiquitina-Conjugadoras/química , Enzimas Ubiquitina-Conjugadoras/metabolismo , Secuencia de Aminoácidos , Animales , Dominio Catalítico , Ciclina B/metabolismo , Evolución Molecular , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Filogenia , Unión Proteica , Estructura Secundaria de Proteína , Alineación de Secuencia , Electricidad Estática , Ubiquitina/metabolismo , Enzimas Ubiquitina-Conjugadoras/clasificación , Enzimas Ubiquitina-Conjugadoras/genética
15.
Transplantation ; 99(2): 385-90, 2015 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-25606786

RESUMEN

BACKGROUND: We have previously shown that qualitative assessment of surface electrostatic potential of HLA class I molecules helps explain serological patterns of alloantibody binding. We have now used a novel computational approach to quantitate differences in surface electrostatic potential of HLA B-cell epitopes and applied this to explain HLA Bw4 and Bw6 antigenicity. METHODS: Protein structure models of HLA class I alleles expressing either the Bw4 or Bw6 epitope (defined by sequence motifs at positions 77 to 83) were generated using comparative structure prediction. The electrostatic potential in 3-dimensional space encompassing the Bw4/Bw6 epitope was computed by solving the Poisson-Boltzmann equation and quantitatively compared in a pairwise, all-versus-all fashion to produce distance matrices that cluster epitopes with similar electrostatics properties. RESULTS: Quantitative comparison of surface electrostatic potential at the carboxyl terminal of the α1-helix of HLA class I alleles, corresponding to amino acid sequence motif 77 to 83, produced clustering of HLA molecules in 3 principal groups according to Bw4 or Bw6 epitope expression. Remarkably, quantitative differences in electrostatic potential reflected known patterns of serological reactivity better than Bw4/Bw6 amino acid sequence motifs. Quantitative assessment of epitope electrostatic potential allowed the impact of known amino acid substitutions (HLA-B*07:02 R79G, R82L, G83R) that are critical for antibody binding to be predicted. CONCLUSIONS: We describe a novel approach for quantitating differences in HLA B-cell epitope electrostatic potential. Proof of principle is provided that this approach enables better assessment of HLA epitope antigenicity than amino acid sequence data alone, and it may allow prediction of HLA immunogenicity.


Asunto(s)
Mapeo Epitopo/métodos , Epítopos , Antígenos HLA-B/química , Antígenos HLA-B/inmunología , Isoanticuerpos/inmunología , Simulación de Dinámica Molecular , Secuencias de Aminoácidos , Sitios de Unión de Anticuerpos , Antígenos HLA-B/metabolismo , Histocompatibilidad , Humanos , Isoanticuerpos/metabolismo , Dominios y Motivos de Interacción de Proteínas , Estructura Secundaria de Proteína , Electricidad Estática , Relación Estructura-Actividad , Propiedades de Superficie
16.
J Inorg Biochem ; 98(7): 1175-82, 2004 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-15219983

RESUMEN

In cytochrome P450s, the active site is situated deep inside the protein next to the heme cofactor, and is often completely isolated from the surrounding solvent. To identify routes by which substrates may enter into and products exit from the active site, random expulsion molecular dynamics simulations were performed for three cytochrome P450s: CYP101, CYP102A1 and CYP107A1 [J. Mol. Biol. 303 (2000) 797; Proc. Natl. Acad. Sci. USA 99 (2002) 5361]. Amongst the different pathways identified, one pathway was found to be common to all three cytochrome P450s although the mechanism of ligand passage along it was different in each case and apparently adapted to the substrate specificity of the enzyme. Recently, a number of new crystal structures of cytochrome P450s have been solved. Here, we analyse the open channels leading to the active site that these structures reveal. We find that in addition to showing the common pathway, they provide experimental evidence for the existence of three additional channels that were identified by simulation. We also discuss how the location of xenon binding sites in CYP101 suggests a role for one of the pathways identified by molecular dynamics simulations as a route for gaseous species, such as oxygen, to access the active site.


Asunto(s)
Sistema Enzimático del Citocromo P-450/química , Hemo/química , Animales , Sitios de Unión , Cristalografía por Rayos X , Humanos , Estructura Terciaria de Proteína
17.
Curr Drug Metab ; 13(2): 143-54, 2012 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-22208529

RESUMEN

The active site of liver-specific, drug-metabolizing cytochrome P450 (CYP) monooxygenases is deeply buried in the protein and is connected to the protein surface through multiple tunnels, many of which were found open in different CYP crystal structures. It has been shown that different tunnels could serve as ligand passage routes in different CYPs. However, it is not understood whether one CYP uses multiple routes for substrate access and product release and whether these routes depend on ligand properties. From 300 ns of molecular dynamics simulations of CYP2C9, the second most abundant CYP in the human liver we found four main ligand exit routes, the occurrence of each depending on the ligand type and the conformation of the F-G loop, which is likely to be affected by the CYP-membrane interaction. A non-helical F-G loop favored exit towards the putative membrane-embedded region. Important protein features that direct ligand exit include aromatic residues that divide the active site and whose motions control access to two pathways. The ligands interacted with positively charged residues on the protein surface through hydrogen bonds that appear to select for acidic substrates. The observation of multiple, ligand-dependent routes in a CYP aids understanding of how CYP mutations affect drug metabolism and provides new possibilities for CYP inhibition.


Asunto(s)
Hidrocarburo de Aril Hidroxilasas/química , Dominio Catalítico , Citocromo P-450 CYP2C9 , Humanos , Ligandos , Simulación de Dinámica Molecular
18.
J Am Soc Mass Spectrom ; 23(12): 2063-74, 2012 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-23055078

RESUMEN

The radical ion chemistry of a suite of S-nitrosopeptides has been investigated. Doubly and triply-protonated ions of peptides NYCGLPGEYWLGNDK, NYCGLPGEYWLGNDR, NYCGLPGERWLGNDR, NACGAPGEKWAGNDK, NYCGLPGEKYLGNDK, NYGLPGCEKWYGNDK and NYGLPGEKWYGCNDK were subjected to electron capture dissociation (ECD), and collision-induced dissociation (CID). The peptide sequences were selected such that the effect of the site of S-nitrosylation, the nature and position of the basic amino acid residues, and the nature of the other amino acid side chains, could be interrogated. The ECD mass spectra were dominated by a peak corresponding to loss of (•)NO from the charge-reduced precursor, which can be explained by a modified Utah-Washington mechanism. Some backbone fragmentation in which the nitrosyl modification was preserved was also observed in the ECD of some peptides. Molecular dynamics simulations of peptide ion structure suggest that the ECD behavior was dependent on the surface accessibility of the protonated residue. CID of the S-nitrosylated peptides resulted in homolysis of the S-N bond to form a long-lived radical with loss of (•)NO. The radical peptide ions were isolated and subjected to ECD and CID. ECD of the radical peptide ions provided an interesting comparison to ECD of the unmodified peptides. The dominant process was electron capture without further dissociation (ECnoD). CID of the radical peptide ions resulted in cysteine, leucine, and asparagine side chain losses, and radical-induced backbone fragmentation at tryptophan, tyrosine, and asparagine residues, in addition to charge-directed backbone fragmentation.


Asunto(s)
Compuestos Nitrosos/química , Péptidos/química , Secuencia de Aminoácidos , Cisteína/química , Gases/química , Iones/química , Simulación de Dinámica Molecular , Datos de Secuencia Molecular , Espectrometría de Masa por Ionización de Electrospray , Espectrometría de Masas en Tándem
19.
J Chem Theory Comput ; 6(5): 1753-68, 2010 May 11.
Artículo en Inglés | MEDLINE | ID: mdl-26615704

RESUMEN

In order to study protein-inorganic surface association processes, we have developed a physics-based energy model, the ProMetCS model, which describes protein-surface interactions at the atomistic level while treating the solvent as a continuum. Here, we present an approach to modeling the interaction of a protein with an atomically flat Au(111) surface in an aqueous solvent. Protein-gold interactions are modeled as the sum of van der Waals, weak chemisorption, and electrostatic interactions, as well as the change in free energy due to partial desolvation of the protein and the metal surface upon association. This desolvation energy includes the effects of water-protein, water-surface, and water-water interactions and has been parametrized using molecular dynamics (MD) simulations of water molecules and a test atom at a gold-water interface. The proposed procedure for computing the energy terms is mostly grid-based and is therefore efficient for application to long-time simulations of protein binding processes. The approach was tested for capped amino acid residues whose potentials of mean force for binding to a gold surface were computed and compared with those obtained previously in MD simulations with water treated explicitly. Calculations show good quantitative agreement with the results from MD simulations for all but one amino acid (Trp), as well as correspondence with available experimental data on the adhesion properties of amino acids.

20.
J Comput Chem ; 20(7): 704-712, 1999 May.
Artículo en Inglés | MEDLINE | ID: mdl-34376033

RESUMEN

A method of modeling polarization by representing an atomic-centered induced dipole as a set of induced charges on the atom and its immediate neighbors is presented. The method is based on earlier work on deriving atomic charges from a distributed multipole analysis (P. J. Winn et al., J Phys Chem A 1997, 101, 5437; G. G. Ferenczy, J Comput Chem 1991, 12, 913). The method has been applied to the water dimer, water trimers, formaldehyde-water complexes, methanol complexes, and DNA basepairs. It was found that the induced charges described the various cooperative and anticooperative hydrogen bonding systems well, both qualitatively and quantitatively (as compared with Hartree-Fock calculations). Importantly, it has been shown that, when an induced charge (or induced dipole) model is used for larger molecules, a correction term is required for the underlying electrostatics. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 704-712, 1999.

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