Computational protocol: Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells

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Protocol publication

[…] The structures of rAls1 and Als3 were modeled using a combination of knowledge- and energy-based methods to avoid limits of any single method in assessing folding of multiple Als domains. Homolog searches were conducted on 100–200 residue blocks of each Als sequence. The domains identified were joined, and the most likely domain configuration was determined by Monte Carlo searches of φ and ψ angles for connecting regions. The domains presented were the consensus of folds identified by Composer [], MatchMaker [], GeneFold [], Robetta [], Fugue [], and Swiss-Model []. The AMBER99 force fields were used throughout these studies to optimize models. AMBER8 [] and SYBYL 7.0–7.2 (Tripos Inc., http://www.tripos.com) were implemented on multiple graphics workstations (Sun Microsystems, Inc., http://www.sun.com; and SGI, Inc., http://www.sgi.com) using LINUX and IRIX operating systems. In addition to the semi-automated procedures above, backbone trajectories were obtained using FASTA searches of the Research Collaboratory for Structural Bioinformatics (RCSB) protein databank (http://www.rcsb.org). Side chains of the target rAls1 and rAls3 models were refined by molecular dynamics and minimization of strain energies, while retaining backbone trajectory by fixing positions of the peptide backbone atoms. The torsion angles of all peptide bonds were adjusted to 180° ± 15°, with minimal constraints. Where appropriate, selected model constraints applied a 0.4-kJ penalty to the Ramachandran φ and ψ angles to enforce regions of predicted α and β structures. Final global energy minimizations were performed for each model after removal of all constraints. Finally, the physicochemical properties of the peptides were visualized by MOLCAD [] as implemented in SYBYL 7.0–7.2 and HINT []. In these utilities, the physical properties of the peptides are superimposed upon the backbone trajectory, or projected onto the water-accessible surface of the molecules. […]

Pipeline specifications

Software tools Robetta, FUGUE, AMBER
Application Protein structure analysis
Organisms Candida albicans, Homo sapiens, Cricetulus griseus
Diseases Oropharyngeal Neoplasms