Carlos A. Del Carpio
Research interests
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InterestsComputational Biology, Computational Biophysics, Genomics, Proteomics, Computational Biochemistry, Computational Drug Designing, Computational Chemistry, Docking Studies, Drug Design, Docking Softwares, QSAR, Docking, Quantum Chemistry, Density Functional Theory, Chemoinformatics, Protein Folding, Computer Aided Drug Design, Homology Modeling
Publications
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Elucidate the origin of CYP flexible structural variation using molecular dynamics calculations
Journal of Toxicology and Environmental Health Sciences. 11/2011; 3(12):335 - 341.
Human cytochrome P450 1A2 (CYP1A2) plays a critical role in the mechanism of drug metabolism the understanding of which constitutes a cornerstone in drug design processes. Its relevance has furthered in view of recent trends in tailor made medicine, since the enzyme's activity differs according ... [more] Human cytochrome P450 1A2 (CYP1A2) plays a critical role in the mechanism of drug metabolism the understanding of which constitutes a cornerstone in drug design processes. Its relevance has furthered in view of recent trends in tailor made medicine, since the enzyme's activity differs according to the mutations or single nucleotide polymorphisms (SNP's) in the respective genetic coding region. Here we investigate the structural variation induced by selected single mutations that have been reported on the CYP1A2 enzyme. We applied our graph theory approach and mainly focus on the differences in 3D structure between the "wild-type" and the mutant structures in terms of the structural flexibility changes that may arise as consequence of the mutations. Based on this information we have additionally inferred internal collective motions that may affect the function of the enzyme using molecular dynamics simulations. Our results show that most of the studied mutations are located in loops and regions of high flexibility and the simulation of their dynamic behavior sheds light on probable consequences of these mutations on the function of the enzyme.
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1.27Impact points
The effect of R249S carcinogenic and H168R-R249S suppressor mutations on p53-DNA interaction, a multi scale computational study.
Computers in biology and medicine. 05/2010; 40(5):498-508.
In this study we have undertaken the theoretical analysis of the effect of R249S carcinogenic and H168R-R249S suppressor mutation at core domain of the tumor suppressor protein p53, on its natural interaction with DNA using a newly developed method. The results show that the carcinogenic mutation R2... [more] In this study we have undertaken the theoretical analysis of the effect of R249S carcinogenic and H168R-R249S suppressor mutation at core domain of the tumor suppressor protein p53, on its natural interaction with DNA using a newly developed method. The results show that the carcinogenic mutation R249S affects the flexibility of L3 loop region in p53, inducing the loss of important hydrogen bonds observed at interaction in the wild-type with DNA, on the other hand the suppressor mutation H168R on the R249S assists in maintaining the wild-type like flexibility of the L3 region in p53 and thus recover the interaction terms lost in the carcinogenic mutation alone. The present study sets a new direction in the development of new drugs that may restore the interactions that lost as a consequence of the carcinogenic mutations in p53.
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1.44Impact points
Quantum chemistry study on absorption spectra, electronic and electrical properties of organic dye on anatase(001).
Journal of nanoscience and nanotechnology. 04/2010; 10(4):2434-43.
As the most reactive surface, the stoichiometric O-bridge terminated anatase(001) surface attracted considerable attentions in many application fields. The interfacial electron transfer in dye-sensitized anatase(001) plays a principal role in a variety of photoinduced reactions. In the present work,... [more] As the most reactive surface, the stoichiometric O-bridge terminated anatase(001) surface attracted considerable attentions in many application fields. The interfacial electron transfer in dye-sensitized anatase(001) plays a principal role in a variety of photoinduced reactions. In the present work, the UV-vis absorption spectrum of TiO2 bulk and different surface models were calculated by means of tight-binding quantum chemical molecular dynamics program "Colors-excite" for the first time. The thickness dependence on electronic and electrical properties of anatase(001) surface was achieved. The anatase(001) surface with a thickness of 1.0 nm shows excellent electronic and electrical properties. Moreover, the most suitable binding mode (dissociative adsorption) and absorption spectra of perylene with acrylic acid (PAA) on the optimum anatase(001) were investigated. A significant red-shift was observed from the UV-vis absorption spectrum of PAA/anatase(001) system. The red-shift occurring when PAA adsorbed on anatase(001) surface suggests that PAA/anatase(001) may be potential candidate for dye-sensitized solar cell. This study also proposed an effective computational tool "Colors-excite" to study of the electronic excitation properties for both molecular and periodic systems.
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1.44Impact points
Tribochemical reaction dynamics of molybdenum dithiocarbamate on nascent iron surface: a hybrid quantum chemical/classical molecular dynamics study.
Journal of nanoscience and nanotechnology. 04/2010; 10(4):2495-502.
Using a hybrid quantum chemical/classical molecular dynamics method, we have studied the tribochemical reaction dynamics of molybdenum dithiocarbamate (MoDTC), a commonly used friction modifier in automobile engine oils. MoDTC molecule adsorbed on rubbing nascent iron surface was situated. We firstl... [more] Using a hybrid quantum chemical/classical molecular dynamics method, we have studied the tribochemical reaction dynamics of molybdenum dithiocarbamate (MoDTC), a commonly used friction modifier in automobile engine oils. MoDTC molecule adsorbed on rubbing nascent iron surface was situated. We firstly investigated the dynamic behavior of MoDTC molecule on the rubbing Fe(001) surface. During the friction simulation, the elongation of Mo-O bonds was observed, forming the Mo2S4 and thiocarbamic acid molecules. To unveil the detailed mechanism of this bond elongation, the electronic states of the MoDTC molecule and Fe(001) surface were computed, and the catalytic effects of Fe(001) surface to the molecule was found. We also found that extreme friction would influence the complete Mo-O bond dissociation. By using the hybrid quantum chemical/classical molecular dynamics method, we successfully simulated the tribochemical reaction dynamics of MoDTC as a friction modifier and obtained the influences of nascent iron surface and friction on its chemical reaction.
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2.34Impact points
A graph theoretical approach for assessing bio-macromolecular complex structural stability.
Journal of molecular modeling. 05/2009;
Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Bas... [more] Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Based on the graph theoretical approach of Jacobs et al. [Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 44:150-165] for expressing molecular flexibility, we propose a new scheme to analyze the structural stability of bio-molecular complexes. This analysis is performed in terms of the identification in interacting subunits of clusters of flappy amino acids (those constituting regions of potential internal motion) that undergo an increase in rigidity at complex formation. Gains in structural rigidity of the interacting subunits upon bio-molecular complex formation can be evaluated by expansion of the network of intra-molecular inter-atomic interactions to include inter-molecular inter-atomic interaction terms. We propose two indices for quantifying this change: one local, which can express localized (at the amino acid level) structural rigidity, the other global to express overall structural stability for the complex. The new system is validated with a series of protein complex structures reported in the protein data bank. Finally, the indices are used as scoring coefficients to rank automatically generated protein complex decoys.
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3.25Impact points
Quantum chemical studies for oxidation of morpholine by Cytochrome P450.
Journal of inorganic biochemistry. 10/2008;
Since morpholine oxidation has recently been shown to involve Cytochrome P450, the study on its mechanism at molecular level using quantum chemical calculations for the model of cytochrome active site is reported here. The reaction pathway is investigated for two electronic states, the doublet and t... [more] Since morpholine oxidation has recently been shown to involve Cytochrome P450, the study on its mechanism at molecular level using quantum chemical calculations for the model of cytochrome active site is reported here. The reaction pathway is investigated for two electronic states, the doublet and the quartet, by means of density functional theory. The results show that morpholine hydroxylation occurs through hydrogen atom abstraction and rebound mechanism. However, in the low spin state, the reaction is concerted and hydrogen atom abstraction yields directly ferric-hydroxy morpholine complex without a distinct rebound step while in quartet state the reaction is stepwise. The presence of nitrogen in a morpholine heterocycle is postulated to greatly facilitate hydrogen abstraction. The hydroxylated product undergoes intramolecular hydrogen atom transfer from hydroxy group to nitrogen, leading to the cleavage of the C-N bond and the formation of 2-(2-aminoethoxy) acetaldehyde. The cleavage of the C-N bond is indicated as the rate-determining step for the studied reaction. The assistance of explicit water molecule is shown to lower the energy barrier for the C-N bond cleavage in enzymatic environment whereas solvent effects mimicked by COSMO solvent model have minor influence on relative energies along the pathway.
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2.34Impact points
Oxidation mechanism in the metabolism of (S)-N-[1-(3-morpholin-4-ylphenyl)ethyl]-3-phenylacrylamide on oxyferryl active site in CYP3A4 Cytochrome: DFT modeling.
Journal of molecular modeling. 08/2007; 13(6-7):851-60.
The metabolism mechanism of (S)-N-[1-(3-morpholin-4ylphenyl)ethyl]-3-phenylacrylamide, mediated by CYP3A4 Cytochrome has been investigated by density functional QM calculations aided with molecular mechanics/molecular dynamics simulations. Two different orientations of phenyl ring for substrate appr... [more] The metabolism mechanism of (S)-N-[1-(3-morpholin-4ylphenyl)ethyl]-3-phenylacrylamide, mediated by CYP3A4 Cytochrome has been investigated by density functional QM calculations aided with molecular mechanics/molecular dynamics simulations. Two different orientations of phenyl ring for substrate approach toward oxyferryl center, imposing two subsequent rearrangement pathways have been investigated. Starting from sigma-complex in perpendicular orientation enzymatic mechanism involves consecutive proton shuttle intermediate, which further leads to the formation of alcohol and ketone. Parallel conformation leads solely to ketone product by 1,2 hydride shift. Although parallel and perpendicular sigma-complexes are energetically equivalent both for the gas phase or PCM solvent model, molecular dynamics studies in full CYP3A4 environment show that perpendicular conformation of the sigma-complex should be privileged, stabilized by hydrophobic interactions of phenylacrylamide chain. After assessing probability of the two conformations we postulate that the alcohol, accessible with the lowest energy barriers should be the major metabolite for studied substrate and CYP3A4 enzyme.
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2.55Impact points
Identification of amino acid residues in the Ah receptor involved in ligand binding.
Biochemical and biophysical research communications. 04/2007; 354(2):396-402.
The Ah receptor (AhR) is a ligand-activated transcription factor. Five amino acids as candidate amino acids necessary for ligand binding within or near the ligand-binding domain were selected based on their evolutional conservation and their aromatic nature that could interact with xenobiotic ligand... [more] The Ah receptor (AhR) is a ligand-activated transcription factor. Five amino acids as candidate amino acids necessary for ligand binding within or near the ligand-binding domain were selected based on their evolutional conservation and their aromatic nature that could interact with xenobiotic ligands. These amino acids were changed to Ala, and the mutated AhRs were subjected to a test of their transactivation activity in HeLa cells. Mutation of Phe318 completely lost its activity whereas other mutations only weakly impaired activity. The Leu-substituted mutant, AhR(Phe318Leu), activated the luciferase activity to the level comparable to wild type in the cells treated with 3-methylcholanthrene (MC) but not at all with beta-naphthoflavone (beta-NF). Ligand-binding activity of mutants was examined with [3H]MC in vitro. AhR(Phe318Ala) could not bind to [3H]MC. [3H]MC bound by AhR(Phe318Leu) was competed with unlabeled MC but not with beta-NF. A structural model of the ligand-binding domain was constructed.
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2.46Impact points
Combinatorial computational chemistry approach for materials design: applications in deNOx catalysis, Fischer-Tropsch synthesis, lanthanoid complex, and lithium ion secondary battery.
Combinatorial chemistry & high throughput screening. 03/2007; 10(2):99-110.
Computational chemistry can provide fundamental knowledge regarding various aspects of materials. While its impact in scientific research is greatly increasing, its contributions to industrially important issues are far from satisfactory. In order to realize industrial innovation by computational ch... [more] Computational chemistry can provide fundamental knowledge regarding various aspects of materials. While its impact in scientific research is greatly increasing, its contributions to industrially important issues are far from satisfactory. In order to realize industrial innovation by computational chemistry, a new concept "combinatorial computational chemistry" has been proposed by introducing the concept of combinatorial chemistry to computational chemistry. This combinatorial computational chemistry approach enables theoretical high-throughput screening for materials design. In this manuscript, we review the successful applications of combinatorial computational chemistry to deNO(x) catalysts, Fischer-Tropsch catalysts, lanthanoid complex catalysts, and cathodes of the lithium ion secondary battery.
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2.65Impact points
Three-dimensional quantitative structure-activity relationship (3 D-QSAR) and docking studies on (benzothiazole-2-yl) acetonitrile derivatives as c-Jun N-terminal kinase-3 (JNK3) inhibitors.
Bioorganic & medicinal chemistry letters. 12/2006; 16(22):5917-25.
Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were developed for 44 (benzothiazole-2-yl) acetonitrile derivatives, inhibiting c-Jun N-terminal kinase-3 (JNK3). It includes molecular field analysis (MFA) and receptor surface analysis (RSA). The QSAR model was develop... [more] Three-dimensional quantitative structure-activity relationship (3D-QSAR) models were developed for 44 (benzothiazole-2-yl) acetonitrile derivatives, inhibiting c-Jun N-terminal kinase-3 (JNK3). It includes molecular field analysis (MFA) and receptor surface analysis (RSA). The QSAR model was developed using 34 compounds and its predictive ability was assessed using a test set of 10 compounds. The predictive 3D-QSAR models have conventional r2 values of 0.849 and 0.766 for MFA and RSA, respectively; while the cross-validated coefficient r(cv)2 values of 0.616 and 0.605 for MFA and RSA, respectively. The results of the QSAR model were further compared with a structure-based analysis using docking studies with crystal structure of JNK3. Ligands bind in the ATP pocket and the hydrogen bond with GLN155 was found to be crucial for selectivity among other kinases. The results of 3D-QSAR and docking studies validate each other and hence, the combination of both methodologies provides a powerful tool directed to the design of novel and selective JNK3 inhibitors.
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3.47Impact points
Tribochemical reaction dynamics of phosphoric ester lubricant additive by using a hybrid tight-binding quantum chemical molecular dynamics method.
The journal of physical chemistry. B. 10/2006; 110(35):17507-11.
To study the atomistic behavior of the phosphoric ester molecule on the nascent Fe surface under boundary lubrication conditions, we adopted a hybrid tight-binding quantum chemical molecular dynamics method. First, we investigated chemical interactions between phosphoric ester and the nascent Fe sur... [more] To study the atomistic behavior of the phosphoric ester molecule on the nascent Fe surface under boundary lubrication conditions, we adopted a hybrid tight-binding quantum chemical molecular dynamics method. First, we investigated chemical interactions between phosphoric ester and the nascent Fe surface. Phosphoric ester was shown to interact with the nascent Fe surface, forming both covalent and ionic bonds. Formation and dissociation dynamics of covalent bonds during tribochemical reaction was clearly observed during the simulation. The effect of friction condition on the tribochemical reaction dynamics was then studied, and it was indicated that friction would influence the formation and the dissociation of covalent bonds. By using a hybrid tight-binding quantum chemical molecular dynamics method, we obtained insights on initial tribochemical reaction processes for the formation of tribofilm from the phosphoric ester molecule on the nascent Fe surface.
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3.47Impact points
First-principles study on proton dissociation properties of fluorocarbon- and hydrocarbon-based membranes in low humidity conditions.
The journal of physical chemistry. B. 10/2006; 110(36):17872-7.
We present a theoretical study on the proton dissociation properties of the membranes for polymer electrolyte fuel cells. A density functional theory method is used to study the influence of fluorocarbon and hydrocarbon backbones on proton dissociation, the interaction of water molecules with the su... [more] We present a theoretical study on the proton dissociation properties of the membranes for polymer electrolyte fuel cells. A density functional theory method is used to study the influence of fluorocarbon and hydrocarbon backbones on proton dissociation, the interaction of water molecules with the sulfonic acid group, and the energy barriers for proton dissociation. Better proton dissociation properties of CH(3)SO(3)H compared to CF(3)SO(3)H are observed from statistical analyses of the optimized structures for both systems. However, the calculated energy barriers for proton dissociation are lower for CF(3)SO(3)H than for the CH(3)SO(3)H system. At the same time, the interaction of water molecules is stronger for CH(3)SO(3)H than for CF(3)SO(3)H. Also, the analysis of the hydrogen-bonding network in both systems shows that the number of hydrogen bonds formed around the sulfonic acid group in CH(3)SO(3)H is larger than that in CF(3)SO(3)H. Therefore, the decrease of the energy barrier with increasing number of coordinating water molecules, pronounced in the case of CH(3)SO(3)H, may lower the barrier, which enhances good proton conductivity of a hydrocarbon-based polymer in low humidity conditions. Thus the hydration ability of a sulfonic acid group is an important factor for realizing better proton dissociation in low humidity conditions.
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1.37Impact points
Molecular dynamics study on the ligand recognition by tandem SH3 domains of p47phox, regulating NADPH oxidase activity.
Computational biology and chemistry. 09/2006; 30(4):303-12.
The phagocyte NADPH oxidase complex plays a crucial role in host defense against microbial infection through the production of superoxides. Chronic granulomatous disease (CGD) is an inherited immune deficiency caused by the absence of certain components of the NADPH oxidase. Key to the activation of... [more] The phagocyte NADPH oxidase complex plays a crucial role in host defense against microbial infection through the production of superoxides. Chronic granulomatous disease (CGD) is an inherited immune deficiency caused by the absence of certain components of the NADPH oxidase. Key to the activation of the NADPH oxidase is the cytoplasmic subunit p47phox, which includes the tandem SH3 domains (N-SH3 and C-SH3). In active phagocytes, p47phox forms a stable complex with the cytoplasmic region of membrane subunit p22phox that forms a left-handed polyproline type-II (PPII) helix conformation. In this report, we have analyzed the conformational changes of p47phox-p22phox complexes of wild-type and three mutants, which have been detected in CGD patients, using molecular dynamics simulations. We have found that in the wild-type, two basal planes of PPII prism in cytoplasmic region of p22phox interacted with N-SH3 and C-SH3. In contrast, in the modeled mutants, the residue at the ape of PPII helix, which interacts simultaneously with both of the tandem SH3 domains in the wild-type, moved toward C-SH3. Furthermore, interaction energies of the cytoplasmic region of p22phox with C-SH3 tend to decrease in these mutants. All these findings led us to conclude that interactions between N-SH3 of p47phox and PPII helix, which is formed by cytoplasmic region of p22phox, may play a significant role in the activation of the NADPH oxidase.
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Robotic path planning and protein complex modeling considering low frequency intra-molecular loop and domain motions.
Genome informatics. International Conference on Genome Informatics. 02/2006; 17(2):270-8.
A novel algorithm is introduced to deal with intra-molecular motions of loops and domains that undergo proteins at interaction with other proteins. The methodology is based on complex energy landscape sampling and robotic motion planning. Mapping high flexibility regions on the protein underlies the... [more] A novel algorithm is introduced to deal with intra-molecular motions of loops and domains that undergo proteins at interaction with other proteins. The methodology is based on complex energy landscape sampling and robotic motion planning. Mapping high flexibility regions on the protein underlies the proposed algorithm. This is the first time this type of research has been reported. Application of the methodology to several protein complexes where remarkable backbone rearrangement is observed shows that the new algorithm is able to deal with the problem of change of backbone conformation at protein interaction. We have implemented the module within the system MIAX (Macromolecular interaction assessment computer system) and together with our already reported soft and flexible docking algorithms we have developed a powerful tool for protein function analysis as part of wide genome function evaluation.
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A graph theoretical approach for analysis of protein flexibility change at protein complex formation.
Genome informatics. International Conference on Genome Informatics. 02/2005; 16(2):148-60.
Hitherto analyses of protein complexes are frequently confined to the changes in the interface of the protein subunits undergoing interaction, while the holistic picture of the protein monomers' structure transformation, or the pervasive rigidity adopted by the newly formed complex are most ofte... [more] Hitherto analyses of protein complexes are frequently confined to the changes in the interface of the protein subunits undergoing interaction, while the holistic picture of the protein monomers' structure transformation, or the pervasive rigidity adopted by the newly formed complex are most often than not improperly evaluated in spite of the multiple and deep insights that they can yield about the interaction process itself at the molecular level, or at the higher level of genomic functional analyses for which relevant systems biological information can be obtained. To address this aspect of protein-protein interaction we propose in this work a newly developed algorithm that is based on graph theoretical instances and makes possible the evaluation of the changes in the flexibility of the interacting molecules and the rigidity adopted at complex formation. Since one can also figure out the opposite process, i.e. that in which the complex decomposes into its constituent subunits, each of which may accomplish another vital role in the organism, the methodology proposed here is also able to address such problem. The algorithm we propose performs a rigidity and/or flexibility evaluation of every node (atom) on the network constituted by the entire set of intra and inter-molecular inter-atomic interactions. Comparison of flexible or rigid molecular regions or domains within the complex with those in the respective isolated monomers leads to quantification of the loss (or gain) in the number of degrees of freedom at complex formation and their effects on protein complex formation mechanisms. This index is also valuable in the identification of collective motions within the protein that may play a critical role in the process of complex formation, and the influences they may have in the behavior and function of the complex (as well as the subunits constituting it) within the organism. Furthermore, the methodology, embedded in protein docking algorithms allows the development of a framework for categorizing and ranking decoys output by broadly used grid scoring type algorithms, one of which is the system for protein-protein interaction system MIAX that has been under continuous development in recent years.
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RNA 3D structure prediction: (1) assessing rna 3D structure similarity from 2D structure similarity.
Genome informatics. International Conference on Genome Informatics. 02/2004; 15(2):112-20.
Computational techniques for 3D structure prediction of proteins, the holy grail of bioinformatics, have undergone major developments in recent years, geared by international cooperation and competition with CASP (Critical Assessment of Structure Prediction Techniques) like contests to improve and r... [more] Computational techniques for 3D structure prediction of proteins, the holy grail of bioinformatics, have undergone major developments in recent years, geared by international cooperation and competition with CASP (Critical Assessment of Structure Prediction Techniques) like contests to improve and refine them. Although straightforward extrapolation of these methodologies for the prediction of the 3D structures of other similarly relevant bio macromolecules may not be too compelling due mostly to the intrinsic differences in constitution, nature, and function between them, the conceptual framework underlying most of those techniques applied to the development of similar computational techniques in structural biology can lead to efficient systems for prediction of the 3D structure of other bio-macromolecules. One of them is the development of rational methodologies to model RNA 3D structures from the sequence of nucleotides composing them. In this paper we establish the fundamentals of a methodology to thread a sequence of nucleotides into a set of 3D fragments extracted from a data base expressly developed for this purpose. The technique is based on a newly implemented algorithm for extraction of 3D fragments by comparison of secondary structures of RNA. The result is a highly efficient system to produce a set of fragments from which entire RNA structure for the given nucleotide sequence can be built.
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Docking unbound proteins with MIAX: a novel algorithm for protein-protein soft docking.
Genome informatics. International Conference on Genome Informatics. 02/2003; 14:238-49.
We propose a new methodology for "soft'' docking unbound protein molecules (reported at the isolated state). The methodology is characterized by its simplicity and easiness of embedment in any rigid body docking process based on point complementarity. It is oriented to allow limited fre... [more] We propose a new methodology for "soft'' docking unbound protein molecules (reported at the isolated state). The methodology is characterized by its simplicity and easiness of embedment in any rigid body docking process based on point complementarity. It is oriented to allow limited free but not unrealistic interpenetration of the side chains of protein surface amino acid residues. The central step to the technique is a filtering process similar to those in image processing. The methodology assists in deletion of atomic-scale details on the surface of the interacting monomers, leading to the extraction of the most characteristic flattened shape for the molecule as well as the definition of a soft layer of atoms to allow smooth interpenetration of the interacting molecules during the docking process. Although the methodology does not perform structural or conformational rearrangements in the interacting monomers, results output by the algorithm are in fair agreement with the relative position of the monomer in experimentally reported complexes. The algorithm performs especially well in cases where the complexity of the protein surfaces is high, that is in hetero dimmer complex prediction. The algorithm is oriented to play the role of a fast screening engine for proteins known to interact but for which no information other than that of the structures at the isolated state is available. Consequently the importance of the methodology will increase in structural-function studies of thousand of proteins derived from large scale genome sequencing projects being executed all around the globe.
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4.20Impact points
A combined bioinformatic approach oriented to the analysis and design of peptides with high affinity to MHC class I molecules.
Immunology and cell biology. 07/2002; 80(3):286-99.
We report on a new method to compute the antigenic degree of peptides from available experimental data on peptide binding affinity to class I MHC molecules. The methodology is a combination of two strategies at different levels of information. The first, at the primary structure level, consists in e... [more] We report on a new method to compute the antigenic degree of peptides from available experimental data on peptide binding affinity to class I MHC molecules. The methodology is a combination of two strategies at different levels of information. The first, at the primary structure level, consists in expressing the peptides binding activity as a profile of amino acid contributions, amino acid similarity being accounted for by their characteristic physicochemical properties and their position within the sequence. The higher level of the strategy is based on a meticulous analysis of the contact interface of the peptides with the cleft constituting the receptor region of a particular class I MHC molecule. Interaction interfaces are inferred by docking the peptide onto the receptor groove of the MHC molecule; evaluation of the affinity of the peptide to the receptor is then performed by analysis of the electrostatic and hydrophobic energies on points of the interaction interface.The result is a robust system for analysis of peptide affinity to class I MHC molecules since while the first analysis dictates the composition of active sequences at the amino acid level, the second translates this information to the atomic level, where the molecular interaction can be analyzed in terms of the intrinsic interatomic forces and energies. Evaluation results for the methodology are encouraging since high affinity peptides are reflected by high scores at both levels of information, and are proportionally lower for peptides of medium and lower affinity for which interaction surfaces show relatively lower electrostatic complementarity and hydrophobic correlation than for the former.
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2.45Impact points
Detection of Chlamydia trachomatis infection with DNA extracted from formalin-fixed paraffin-embedded tissues.
Diagnostic microbiology and infectious disease. 06/2002; 43(1):1-6.
It is a well-known fact that tubal stenosis and/or peritubal adhesion are often associated with Chlamydia trachomatis infection. Although tubal pregnancy may be attributed to this infection, there are only extremely rare cases in which the presence of C. trachomatis has been confirmed by immumo-hist... [more] It is a well-known fact that tubal stenosis and/or peritubal adhesion are often associated with Chlamydia trachomatis infection. Although tubal pregnancy may be attributed to this infection, there are only extremely rare cases in which the presence of C. trachomatis has been confirmed by immumo-histochemical examination on tissues isolated from patients with tubal pregnancy. We thus tried to confirm the presence of C. trachomatis infection by detecting DNA of the organism in tissues surgically isolated from patients with tubal pregnancy.Two detection methods, a ligase chain reaction (LCR) method and an immuno-histochemical staining which detects an antigen of C. trachomatis, were compared using paraffin-embedded tissue samples which were surgically isolated from patients with tubal pregnancy or hydrosalpinx. The LCR method was capable of detecting DNA of C. trachomatis in tissue samples in which the C. trachomatis-specific antigen could not be detected using immuno-histochemical staining. This was due to the fact that immuno-histochemical staining methods are applicable to the analysis of sequences the length of which range from 200 to 400 bp (base pairs), while the LCR method used here allows the analysis of sequences as small as 48 bp. This fact makes the LCR method a very convenient tool, as compared with immuno-histochemical methods, for analysis of the paraffin embedded tissue samples where by effects of formalin--used for fixation for pathologic diagnosis--the risk of fragmenting the DNA samples is relatively high. Presence of C. trachomatis DNA as detected by LCR method in surgically isolated samples from patients with tubal pregnancy supports the involvement of Chlamydia trachomatis infection in the occurrence of tubal pregnancy. Accordingly the LCR method is capable of detecting DNA of C. trachomatis in paraffin-embedded samples of tubal tissue in which presence of C. trachomatis could not be confirmed by an immuno-histochemical staining method.
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Design of an Apoptosis-Inducing Short Peptide Using the System for Macromolecular Interaction Assessment MIAX
03/2001;
Introduction From a practical point of view, the developmX t of newbio-informMM] tools should be directed to assist andeconom1E experim1 tal e#orts or supply themeE[ ds to achievesom/1XEz that cannot be obtained by experim/ t. Recently we have reported on the developm t of anautomOEz system for mE1.... [more] Introduction From a practical point of view, the developmX t of newbio-informMM] tools should be directed to assist andeconom1E experim1 tal e#orts or supply themeE[ ds to achievesom/1XEz that cannot be obtained by experim/ t. Recently we have reported on the developm t of anautomOEz system for mE1.MEzX1.1 interaction assessmn t MIAX [2], having as goal the prediction of the interaction patternamte bio-m[.[EzX/ Here we describe one application of MIAX, taking asexam1] the design of a short peptide to induce apoptosis in cells by binding to the FASm[/]Ez 2 Methodology Fas/APO-1 is atransmE brane protein belonging to thetum[ necrosis factor receptorfampt . FAS/APO1 was initially characterized bymX which is known to induceprogram]M cell death or apoptosis in a variety of susceptibletumc cells. pitopes targeted by Fas ligand as well as the prototypic apoptosis inducing anti-Fas mE CH-11 have been already biochem]M1Ez characterized [3]. ThemeE dology to design a sho
Following (24)
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Abdul Rajjak Shaikh
King Abdullah University of Science and Technology -
Mohamed Ismael
Sohag University -
Osamu Mizuno
Kyoto Institute of Technology -
Toshiharu Akino
Kyoto Institute of Technology -
Sr. N. Uddin Apu
Khulna University
Topics (19)
