Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Homology modelling”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources
PubMed2005

Homology modeling of a transcriptional regulator SoxR of the Lithotrophic sulfur oxidation (Sox) operon in alpha-proteobacteria.

Microbial oxidation of reduced inorganic sulfur compounds in the environment is one of the major reactions of the global sulfur cycle mediated by phylogenetically diverse prokaryotes. The sulfur oxidizing gene cluster (sox) of alpha-Proteobacteria comprises of at least 15 genes, which form two transcriptional units, viz soxSRT and soxVWXYZABCDEFGH. Sequence analysis reveals that SoxR belongs to the ArsR family of helix-turn-helix DNA binding proteins. Although SoxR proteins do not contain the conserved metal-binding box, ELCVCDL, but there are a number of well conserved residues present throughout the sequence that are previously identified in the known ArsR family proteins. We employed homology modeling to construct the three-dimensional structure of the SoxR from chemolithotrophic alpha-Proteobacteria Pseudaminobacter salicylatoxidans KCT001. The predicted homology model of SoxR shows an overall structural similarity with winged helix-turn-helix family proteins. Since dimerization is essential for DNA binding and repression by the ArsR family proteins we have generated the dimeric model of SoxR that enables us to predict the DNA binding residues of the protein as well as the interaction of SoxR with the predicted promoter region of sox gene cluster.

Alphaproteobacteria↗
PubMed1997

Homology modelling of two subtilisin-like proteases from the hyperthermophilic archaea Pyrococcus furiosus and Thermococcus stetteri.

The hyperthermophilic archaeon Pyrococcus furiosus produces an extracellular, glycosylated hyperthermostable subtilisin-like serine protease, termed pyrolysin (Voorhorst,W.G.B., Eggen,R.I.L., Geerling,A.C.M., Platteeuw,C., Siezen,R.J. and de Vos,W.M. (1996) J. Biol. Chem., 271, 20426-20431). Based on the pyrolysin coding sequence, a pyrolysin-like gene fragment was cloned and characterized from the extreme thermophilic archaeon Thermococcus stetteri. Like pyrolysin, the deduced sequence of this serine protease, designated stetterlysin, contains a catalytic domain with high homology with other subtilases, allowing homology modelling starting from known crystal structures. Comparison of the predicted three-dimensional models of the catalytic domain of stetterlysin and pyrolysin with the crystal structure of subtilases from mesophilic and thermophilic origin, i.e. subtilisin BPN' and thermitase, and the homology model of subtilisin S41 from psychrophilic origin, led to the identification of features that could be related to protein stabilization. Higher thermostability was found to be correlated with an increased number of residues involved in pairs and networks of charge-charge and aromatic-aromatic interactions. These highly thermostable proteases have several extra surface loops and inserts with a relatively high frequency of aromatic residues and Asn residues. The latter are often present in putative N-glycosylation sites. Results from modelling of known substrates in the substrate-binding region support the broad substrate range and the autocatalytic activation previously suggested for pyrolysin.

Amino Acid Sequence↗
PubMed1998

Homology model for oncostatin M based on NMR structural data.

Oncostatin M (OM) is a member of the cytokine family which regulates the proliferation and differentiation of a variety of cell types and includes interleukin-6 (IL-6), leukemia inhibitory factor (LIF), and granulocyte-colony stimulating factor (G-CSF). This family of proteins adopts a four-helix bundle fold with up-up-down-down topology and contains intramolecular disulfide bonds. Since an X-ray or NMR structure for OM is not currently available, a homology model for OM was determined from the X-ray structures of human growth hormone (hGH), LIF, and G-CSF where the alignment was based on secondary structure instead of sequence. The OM secondary structure was determined from NMR structural data, and the secondary structures for hGH, LIF, and G-CSF were obtained from the reported X-ray structures. The resulting homology model was refined using sequential NOE distance 13C restraints, chemical shift information, and a conformational database.

Amino Acid Sequence↗
PubMed2006

Ligand-based homology modeling as attractive tool to inspect GPCR structural plasticity.

G protein-coupled receptors (GPCRs) represent the largest family known of signal-transducing molecules. They convey signals for light and many extracellular regulatory molecules. GPCRs have been found to be dysfunctional/dysregulated in a growing number of human diseases and they have been estimated to be the targets of more than 40% of the drugs used in clinical medicine today. The crystal structure of rhodopsin provides the first three-dimensional GPCR information, which now supports homology modeling studies and structure-based drug design approaches. Here, we review our recent work on adenosine receptors, a family of GPCRs and, in particular, on A(3) adenosine receptor subtype antagonists. We will focus on an alternative approach to computationally explore the multi-conformational space of the antagonist-like state of the human A(3) receptor. We define ligand-based homology modeling as new approach to simulate the reorganization of the receptor induced by the ligand binding. The success of this approach is due to the synergic interaction between theory and experiment.

Adenosine A3 Receptor Antagonists↗
PubMed2001

Homology modelling and structural analysis of human arylamine N-acetyltransferase NAT1: evidence for the conservation of a cysteine protease catalytic domain and an active-site loop.

Arylamine N-acetyltransferases (EC 2.3.1.5) (NATs) catalyse the biotransformation of many primary arylamines, hydrazines and their N-hydroxylated metabolites, thereby playing an important role in both the detoxification and metabolic activation of numerous xenobiotics. The recently published crystal structure of the Salmonella typhimurium NAT (StNAT) revealed the existence of a cysteine protease-like (Cys-His-Asp) catalytic triad. In the present study, a three-dimensional homology model of human NAT1, based upon the crystal structure of StNAT [Sinclair, Sandy, Delgoda, Sim and Noble (2000) Nat. Struct. Biol. 7, 560-564], is demonstrated. Alignment of StNAT and NAT1, together with secondary structure predictions, have defined a consensus region (residues 29-131) in which 37% of the residues are conserved. Homology modelling provided a good quality model of the corresponding region in human NAT1. The location of the catalytic triad was found to be identical in StNAT and NAT1. Comparison of active-site structural elements revealed that a similar length loop is conserved in both species (residues 122-131 in NAT1 model and residues 122-133 in StNAT). This observation may explain the involvement of residues 125, 127 and 129 in human NAT substrate selectivity. Our model, and the fact that cysteine protease inhibitors do not affect the activity of NAT1, suggests that human NATs may have adapted a common catalytic mechanism from cysteine proteases to accommodate it for acetyl-transfer reactions.

Acetyltransferases↗
PubMed2005

Humanization by variable domain resurfacing and grafting on a human IgG4, using a new approach for determination of non-human like surface accessible framework residues based on homology modelling of variable domains.

Many antithrombotic agents have only a small therapeutic window, frequently leading to bleeding problems. However, interfering with platelet adhesion through the collagen-VWF-GPIbalpha axis is expected to cause less bleeding problems. Our group developed a monoclonal antibody, 82D6A3, directed against the von Willebrand factor (VWF) A3-domain, which inhibits the VWF-interaction to fibrillar collagen. 82D6A3 has antithrombotic effects in vivo without bleeding time prolongation. To further investigate the promising features of 82D6A3, we have humanized it by variable domain resurfacing and grafting on the constant regions of a human IgG4. First, the sequence of the variable domains was determined and the murine scFv was constructed. The expressed scFv had a comparable activity as the IgG of 82D6A3, and its DNA was thus used in subsequent humanization procedures. For this, a new approach was introduced to identify non-human like framework surface residues, since the general distribution of accessible residues described for human and murine heavy and light chain variable domains showed several discrepancies with the homology modelled Fv of 82D6A3. Identification of non-human like framework residues and evaluation of their surface accessibility within the context of the homology modelled Fv of 82D6A3, revealed 10 residues that need to be humanized without influencing the conformation of the CDR loops. Indeed, the humanized scFv of 82D6A3, obtained by mutating all 10 residues to their human counterpart, was still binding with high affinity to VWF and retained the inhibitory properties of the murine scFv. Next, in order to increase its half life and to decrease its immunogenicity, the humanized variable domains were grafted on the constant regions of a human IgG4, resulting in h82D6A3 with an in vitro activity comparable to that of the murine IgG.

Amino Acid Sequence↗
PubMed1998

Homology modeling of the receptor binding domain of human thrombopoietin.

Platelet production in blood is regulated by a lineage specific humoral factor, thrombopoietin (TPO). The amino terminal domain of TPO (TPO-N) is responsible for the signal transduction mediated by the TPO receptor, c-mpl. From the predicted length of helices we found that TPO-N belongs to the long-chain subfamily of the four-helix bundle cytokine family. We built a three dimensional model of TPO-N by a comparative homology modeling procedure. The four helices of TPO-N with an up-up-down-down topology are stabilized by a tightly packed central hydrophobic core and the extended loop AB makes an additional hydrophobic core with helices B and D outside of the four helix bundle scaffold. An interpretation of the previous site directed mutageneses results in light of the model enabled us to identify two isolated receptor binding sites. The surface made of Lys 136, Lys 138 and Lys 140 in helix D, and Pro 42 and Glu 50 in loop AB forms the first receptor binding site, while the surface of Asp 8, Arg 10 and Lys 14 in helix A represents the second binding site for the sequential receptor oligomerization.

Disulfides↗
PubMedDate not supplied

Structure and specificity of a human valacyclovir activating enzyme: a homology model of BPHL.

Biphenyl hydrolase-like (BPHL) protein is a novel serine hydrolase which has been identified as human valacyclovirase (VACVase), catalyzing the hydrolytic activation of valine ester prodrugs of the antiviral drugs acyclovir and ganciclovir as well as other amino acid ester prodrugs of therapeutic nucleoside analogues. The broad specificity for nucleoside analogues as parent drugs suggests that BPHL may be particularly useful as a molecular target for prodrug activation. In order to develop an initial structural view of the specificity of BPHL, a homology model of BPHL based on the crystal structure of 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase was developed using the Molecular Operating Environment package (Chemical Computing Group, Montreal, Quebec), evaluated for its stereochemical quality and identification of free cysteines, and used in a molecular docking study. The BPHL model has residues S122, H255, and D227 comprising the putative catalytic triad in proximity and potential charge-charge interaction sites, M52 or D123 for the alpha-amino group. The model also suggested that the structural preference of BPHL for hydrophobic amino acyl promoieties and its limited activity for the secondary alcohol substrates may be attributed to the hydrophobic acyl-binding site formed by residues I158, G161, I162, and L229, and the spatial constraint around the catalytic site by a loop on one side, the active serine and histidine on the other side, and L53 and L179 on top. In addition, the broad specificity for nucleoside analogues may be due to the relatively less constrained nucleoside-binding site opening toward the entrance of the substrate-binding pocket. The homology model of BPHL provides a basis for further investigation of the catalytic and active site residues, can account for the observed structure activity profile of BPHL, and will be useful in the design of nucleoside prodrugs.

Acyclovir↗
PubMed2001

[Activation of ATP-sensitive K+ channels by ADP and K+ channel openers: homology model of sulfonylurea receptor carboxyl-termini].

The ATP-sensitive K+ channels (KATP) are composed of Kir6.0 subunits and sulfonylurea receptors (SUR1, 2A and 2B). SUR2A and SUR2B are splice variants and differ only in the C-terminal 42 amino acid residue (C42). SURs are supposed to be the subunit that determines the different response of KATPs to intracellular nucleotides, K+ channel openers and inhibitors. In this study, we report that C42 of SURs plays critical roles in differential activation of various KATPs by ADP and K+ channel openers such as diazoxide and nicorandil. KATPs containing distinct SURs and Kir6.2 were reconstructed on HEK293T cells. Much higher concentrations of ADP were necessary to activate channels which SUR1 or SUR2B. In all KATPs containing different SUR, diazoxide increased the potency of ADP for channel activity without affecting its efficacy. From the electrophysiological data obtained from C-terminal chimeras and point mutants in the second nucleotide binding domain (NBDs), we developed the homology model of each SUR-NBD2 based on the crystallgraphically determined structure of HisP, a member of the ABC protein superfamily. In this model, C42 is located just beneath the Walker A motif of NBD2 and regulates the binding of nucleotide to NBD2 by affecting the 3-D construct of NBD2. This homology model well explains the different response of KATPs to ADP. Based on this model, it will be possible to develop new ligands for KATPs.

ATP-Binding Cassette Transporters↗
PubMed1996

How similar must a template protein be for homology modeling by side-chain packing methods?

Given the correct backbone coordinates of a globular protein, side-chain packing methods can be generally expected to predict the side-chain coordinates of the buried core residues accurately. In the context of a study in modeling a family of bacteriophage DNA-binding proteins, we observed that when the coordinates of the actual perfect backbone are not available, the side-chain packing methods are still of predictive value using homologous but imperfect backbones. This is the situation in practical homology modeling where a target protein sequence is modeled from template structures of known protein homologs. In order to assess the quality and degree of accuracy of such predictions and their dependence on the extent of homology, we have now extended these studies to a well characterized family of globin structures that span a much wider range of sequence-structure similarity. The collective results show a clear relationship that is independent of protein family between side-chain prediction accuracy and the level of similarity between the template and target proteins. We judge this similarity in terms of sequence identity and the backbone r.m.s. deviation of the template structure used for modeling and the actual target structure in cases where the target structures are available. In summary, as sequence identity drops from 100% to about 50%, or when the backbone r.m.s. deviation between template and target structures increases from 0 A to about 1 A, the overall average r.m.s. error for the buried-core residues rises from 1.2 A to 1.5 A while the chi 1 prediction accuracy drops from 85% to 70-75% and the chi 2 prediction accuracy drops from 80% to 60-65%. When the sequence identity drops below 50% or the backbone r.m.s. deviation rises above 1 A, all 3 measures of prediction accuracy decrease rapidly. When the sequence identity edges to the so-called twilight zone of sequence similarity at around 22%, or when the backbone r.m.s. deviation exceeds 2 A, the prediction accuracy approaches the values to be expected for random predictions, namely, 3.1 A for average r.m.s. error, 22% and 29% for accuracy of chi 1 and chi 2 prediction. These observations provide a practical evaluation of the side-chain packing methods and are of value to the homology-modeler. The extent and degree to which the backbone topology of a protein fold can constrain internal side-chain orientation gives insight into the plasticity of the sequence-structure relationship found in the architecture of proteins.

Amino Acid Sequence↗
PubMed2006

Structural insights into the ATP binding pocket of the anaplastic lymphoma kinase by site-directed mutagenesis, inhibitor binding analysis, and homology modeling.

Anaplastic lymphoma kinase (ALK) is a valid target for anticancer therapy; however, potent ALK inhibitors suitable for clinical use are lacking. Because the majority of described kinase inhibitors bind in the ATP pocket of the kinase domain, we have characterized this pocket in ALK using site-directed mutagenesis, inhibition studies, and molecular modeling. Mutation of the gatekeeper residue, a key structural determinant influencing inhibitor binding, rendered the fusion protein, NPM/ALK, sensitive to inhibition by SKI-606 in the nanomolar range, while PD173955 inhibited the NPM/ALK mutant at micromolar concentrations. In contrast, both wild type and mutant NPM/ALK were insensitive to imatinib. Computer modeling indicated that docking solutions obtained with a homology model representing the intermediate conformation of the ALK kinase domain reflected closely experimental data. The good agreement between experimental and virtual results indicate that the ALK molecular models described here are useful tools for the rational design of ALK selective inhibitors. In addition, 4-phenylamino-quinoline compounds may have potential as templates for ALK inhibitors.

Adenosine Triphosphate↗
PubMed2000

An automatic homology modeling method consisting of database searches and simulated annealing.

We introduce a method of homology modeling consisting of database searches and simulated annealing. All processes involving searches for homologous proteins, alignment, the construction of Calpha atoms, construction of main-chain atoms, and the construction of side-chain atoms are performed automatically. In this method, main-chain conformations are generated from the weighted average of mainchain coordinates in reference proteins. The weight is defined by the local space homology representing the similarity of environmental residues at topologically equivalent positions in reference proteins. Side-chain conformations are generated for constructed main-chain atoms by database searches, and main-chain atoms are optimized for the fixed side-chain conformations. These two processes, i.e., the side-chain generation and main-chain optimization, are repeated several times. This type of construction provides a structure similar to the x-ray structure, in particular, for main-chain and side-chain atoms in the residues belonging to structurally conserved regions (SCRs). The accuracy of our method was evaluated for 14 proteins whose structures are known. The average root mean square deviation between models and x-ray structures was 2.29 A for all atoms, and the percentage of chi1 angles within 30 degrees was 72.6% for SCRs residues. Some models were in good agreement with their respective x-ray structures. Our method, which has the advantage of being automated, gives results similar to, or better than, published results for three widely used test proteins. Our software, FAMS, is available on the World Wide Web.

Amino Acid Sequence↗
PubMed2003

The three-dimensional solution structure of NaD1, a new floral defensin from Nicotiana alata and its application to a homology model of the crop defense protein alfAFP.

NMR spectroscopy and simulated annealing calculations have been used to determine the three-dimensional structure of NaD1, a novel antifungal and insecticidal protein isolated from the flowers of Nicotiana alata. NaD1 is a basic, cysteine-rich protein of 47 residues and is the first example of a plant defensin from flowers to be characterized structurally. Its three-dimensional structure consists of an alpha-helix and a triple-stranded antiparallel beta-sheet that are stabilized by four intramolecular disulfide bonds. NaD1 features all the characteristics of the cysteine-stabilized alphabeta motif that has been described for a variety of proteins of differing functions ranging from antibacterial insect defensins and ion channel-perturbing scorpion toxins to an elicitor of the sweet taste response. The protein is biologically active against insect pests, which makes it a potential candidate for use in crop protection. NaD1 shares 31% sequence identity with alfAFP, an antifungal protein from alfalfa that confers resistance to a fungal pathogen in transgenic potatoes. The structure of NaD1 was used to obtain a homology model of alfAFP, since NaD1 has the highest level of sequence identity with alfAFP of any structurally characterized antifungal defensin. The structures of NaD1 and alfAFP were used in conjunction with structure-activity data for the radish defensin Rs-AFP2 to provide an insight into structure-function relationships. In particular, a putative effector site was identified in the structure of NaD1 and in the corresponding homology model of alfAFP.

Amino Acid Sequence↗
PubMed2005

A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains.

PDZ domains are important scaffolding modules that typically bind to the C-termini of their interaction partners. Several structures of such complexes have been solved, revealing a conserved binding site in the PDZ domain and an extended conformation of the bound peptide. A compendium of information regarding PDZ complexes demonstrates that dissimilar C-terminal peptides bind to the same PDZ domain, and different PDZ domains can bind the same peptides. A detailed understanding of the PDZ-peptide recognition is needed to elucidate this complexity. To this end, we have designed a family of docking protocols for PDZ domains (termed PDZ-DocScheme) that is based on simulated annealing molecular dynamics and rotamer optimization, and is applicable to the docking of long peptides (20-40 rotatable bonds) to both known PDZ structures and to the more complicated problem of homology models of these domains. The resulting protocol reproduces the structures of PDZ complexes with peptides 4-8 amino acids long within 1-2 A from the experimental structure when the docking is performed to the original structure. If the structure of the target PDZ domain is an apo structure or a homology model, the docking protocol yields structures within 3 A in 9 out of 12 test cases. The automated docking procedure PDZ-DocScheme can serve in the generation of a structural context for validation of PDZ domain specificity from mutagenesis and ligand binding data.

Models, Molecular↗
PubMed2001

Analysis of a three-dimensional structure of Potato leafroll virus coat protein obtained by homology modeling.

Viruses of the family Luteoviridae are ssRNA plant viruses that have particles that exhibit icosahedral symmetry. To identify the residues that might be exposed on the surface of the Potato leafroll virus (PLRV; genus Polerovirus, family Luteoviridae) capsid, and therefore involved in biological interactions, we performed a structural analysis of the PLRV coat protein (CP) on the basis of comparisons with protein sequences and known crystal structures of CPs of other viruses. The CP of PLRV displays 33% sequence similarity with that of Rice yellow mottle virus (genus Sobemovirus) when the sequences were aligned by using the hidden Markov model method. A structure model for PLRV CP was designed by protein homology modeling, using the crystal structure of RYMV as a template. The resulting model is consistent with immunological and site-directed mutagenesis data previously reported. On the basis of this model it is possible to predict some surface properties of the PLRV CP and also speculate about the structural evolution of small icosahedral viruses.

Amino Acid Sequence↗
PubMed1999

Homology modeling of the multicopper oxidase Fet3 gives new insights in the mechanism of iron transport in yeast.

Fet3, the multicopper oxidase of yeast, oxidizes extracellular ferrous iron which is then transported into the cell through the permease Ftr1. A three-dimensional model structure of Fet3 has been derived by homology modeling. Fet3 consists of three cupredoxin domains joined by a trinuclear copper cluster which is connected to the blue copper site located in the third domain. Close to this site, which is the primary electron acceptor from the substrate, residues for a potential iron binding site could be identified. The surface disposition of negatively charged residues suggests that Fet3 can translocate Fe(3+) to the permease Ftr1 through a pathway under electrostatic guidance.

Amino Acid Sequence↗
PubMed2005

Homology modeling of cytochrome P450scc and the mutations for optimal amperometric sensor.

A new homology model of bovine cytochrome P450scc is obtained starting from the recently determined crystal structure of mammalian cytochrome P450 2B4. The new emerging structure appears compatible with recent diffraction patterns of bovine P450scc microcrystals as obtained at the Microfocus Beamline of the European Synchrotron Radiation in Grenoble and here reported for the first time. The same atomic structure is utilized thereby to predict the mutations needed for modifying redox potential. A comprehensive comparison is finally carried out with the previous model present in the RCSB Protein DataBank also in terms of the alternative mutations being predicted for the same functional modification. The implication of these studies for optimal sensor construction is discussed.

Animals↗
PubMed2004

Characterization of the CYP2C8 active site by homology modeling.

To compare the features of the active sites of CYP2C8, CYP2C9, and CYP2C19, homology modeling was performed based on the crystallographic coordinates of mammalian CYP2C5. It was found that CYP2C8 has a much larger pocket than the other forms due to the existence of an additional pocket. The approach to the additional pocket is comprised of Ile102, Ser114, Leu208, Val366, and Ile476, and the side chains of Ser114, Val366, and Ile476, which are smaller than the corresponding residues in the other CYPs, enable access to the pocket. The general features of the active site in the CYP2C8 model are similar to those of the previously constructed CYP3A4 model, which may account for the 2 CYPs sharing some of their substrates. The CYP2C8 model was validated by examining the bound orientation of paclitaxel and showing that it is consistent with the formation of the 6-beta hydroxylated derivative during metabolism. Docked paclitaxel was found to form a hydrogen bond with the side chain of Asn 99, which is a characteristic residue of CYP2C8 and is located in the additional pocket. Descriptors for CYP2C8 and CYP2C9 substrates were also examined with the molecular operating environment (MOE). The descriptor by which CYP2C8 and CYP2C9 substrates were classified most distinctly was found to be molar refractivity, which might be related to the longer shape and more polar nature of the active site of CYP2C8 in the CYP2C subfamily.

Amino Acid Sequence↗