Comparative protein structure modeling using MODELLER

University of California at San Francisco, San Francisco, California, USA.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 12/2007; Chapter 2(Chapter 5):Unit 2.9. DOI: 10.1002/0471140864.ps0209s50
Source: PubMed


Functional characterization of a protein sequence is a common goal in biology, and is usually facilitated by having an accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described.

Download full-text


Available from: Marc Marti-Renom, Oct 02, 2015
255 Reads
  • Source
    • "We developed scripts and tools which implement the mathematical framework of sampling, use the existing tools to compute the QOIs [10] [12] [2] [18] [44], compute uncertainty bounds as well the visualization directives which can be directly loaded into existing molecular, surface and volume visualization software [3] [38]. Our methods should enable the end user of these tools achieve a more quantitative and visual evaluation of various molecular models for structural and property correctness, or the lack thereof. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Computational molecular modeling and visualization has seen significant progress in recent years with sev- eral molecular modeling and visualization software systems in use today. Nevertheless the molecular biology community lacks techniques and tools for the rigorous analysis, quantification and visualization of the associated errors in molecular structure and its associated properties. This paper attempts at filling this vacuum with the introduction of a systematic statistical framework where each source of structural uncertainty is modeled as a ran- dom variable (RV) with a known distribution, and properties of the molecules are defined as dependent RVs. The framework consists of a theoretical basis, and an empirical implementation where the uncertainty quantification (UQ) analysis is achieved by using Chernoff-like bounds. The framework enables additionally the propagation of input structural data uncertainties, which in the molecular protein world are described as B-factors, saved with almost all X-ray models deposited in the Protein Data Bank (PDB). Our statistical framework is also able and has been applied to quantify and visualize the uncertainties in molecular properties, namely solvation interfaces and solvation free energy estimates. For each of these quantities of interest (QOI) of the molecular models we provide several novel and intuitive visualizations of the input, intermediate, and final propagated uncertainties. These methods should enable the end user achieve a more quantitative and visual evaluation of various molecular PDB models for structural and property correctness, or the lack thereof.
  • Source
    • "Homology models of zebrafish CYP1A, CYP1B1, CYP1C1, CYP1C2 and CYP1D1 were constructed using Modeller 9v8 [38], based on the crystal structures of human CYP1A2 [39] and CYP1B1 [40]. The N-terminal membrane anchor regions of the fish CYP1A sequences were truncated to match the sequence of the human structure. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Zebrafish express five cytochrome P450 1 genes: CYP1A, CYP1B1, CYP1C1, CYP1C2, inducible by aryl hydrocarbon receptor agonists, and CYP1D1, a constitutively expressed CYP1A-like gene. We examined substrate selectivity of CYP1s expressed in yeast. CYP1s were expressed in W(R) yeast, engineered to over-express P450 reductase, via pYES/DEST52 and via pYeDP60. Microsomal fractions from transformed yeast were examined for activity with fluorogenic substrates, benzo[a]pyrene and testosterone. Modeling and docking approaches were used to further evaluate sites of oxidation on benzo[a]pyrene and testosterone. CYP1s expressed in yeast dealkylated ethoxy-, methoxy-, pentoxy- and benzoxy-resorufin (EROD, MROD, PROD, BROD). CYP1A and CYP1C2 had the highest rates of EROD activity, while PROD and BROD activities were low for all five CYP1s. The relative rates of resorufin dealkylation by CYP1C1, CYP1C2 and CYP1D1 expressed via pYeDP60 were highly similar to relative rates obtained with pYES/DEST52-expressed enzymes. CYP1C1 and CYP1C2 dealkylated substituted coumarins and ethoxy-fluorescein-ethylester, while CYP1D1 did not. The CYP1Cs and CYP1D1 co-expressed with epoxide hydrolase oxidized BaP with different rates and product profiles, and all three produced BaP-7,8,9,10-tetrol. The CYP1Cs but not CYP1D1 metabolized testosterone to 6ß-OH-testosterone. However, CYP1D1 formed an unidentified testosterone metabolite better than the CYP1Cs. Testosterone and BaP docked to CYP homology models with poses consistent with differing product profiles. Yeast-expressed zebrafish CYP1s will be useful in determining further functionality with endogenous and xenobiotic compounds. Determining the roles of zebrafish CYP1s in physiology and toxicology depends on knowing the substrate selectivity of these enzymes. Copyright © 2015. Published by Elsevier B.V.
    Biochimica et Biophysica Acta 07/2015; 1850(11). DOI:10.1016/j.bbagen.2015.07.010 · 4.66 Impact Factor
  • Source
    • "Model building involved use of MODELLER v9.14 with the graphic user interface program EASYMODELLER 4.0 (Kuntal et al., 2010). The target models of Hsp70 and Hsp90 were generated and refined according to the loop database in MODELLER v9.14 (Eswar et al., 2006). All modelled protein structures were analyzed by use of Swiss-PDB (Guex and Peitsch, 1997). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Heat shock proteins (HSPs) are essential molecular chaperones that are highly conserved across organisms. They have a pivotal function in responding to thermal stress and are responsible for many cellular functions. Here, we aimed to elucidate the possible roles of Hsp70 and Hsp90 in the life cycle of the parasitic nematode Anisakis, particularly third- and fourth-stage larvae, from cold-blooded fish to warm-blooded marine mammals or accidentally to human hosts. We examined the expression profiles of Hsp70 and Hsp90 in different developmental stages of Anisakis pegreffii. The open reading frame of Hsp70 of A. pegreffii was 1950bp, and deduced amino acid sequence showed high homology with those of other nematodes. Heatmap analysis revealed sequence identity of Hsp70 and Hsp90 in 13 important parasitic species, human and yeast. On heatmap and phylogenetic analysis, ApHsp70 and ApHsp90 shared the highest amino acid sequence identity with other nematodes and formed a monophyletic clade. The three-dimensional (3D) structure prediction of the newly characterized ApHsp70 and known ApHsp90 gene showed highly conserved motifs between A. pegreffii and other species. Quantitative real-time PCR and western blot analysis revealed higher mRNA and protein expression for ApHsp70 and ApHsp90 in fourth- than third-stage larvae, with higher mRNA and protein expression for ApHsp70 than ApHsp90. ApHsp70 and ApHsp90 may play important roles in Anisakis in response to thermal stress and might be important molecules in the development of A. pegreffii, which has implications for its control. Copyright © 2015 Elsevier B.V. All rights reserved.
    Veterinary Parasitology 07/2015; DOI:10.1016/j.vetpar.2015.07.006 · 2.46 Impact Factor
Show more