Biomaterial Database

Modeling of Multimolecular Complexes. 2020

Dina Schneidman-Duhovny, and Haim J Wolfson

School of Computer Science and Engineering and the Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.

Macromolecular complexes play a key role in cellular function. Predicting the structure and dynamics of these complexes is one of the key challenges in structural biology. Docking applications have traditionally been used to predict pairwise interactions between proteins. However, few methods exist for modeling multi-protein assemblies. Here we present two methods, CombDock and DockStar, that can predict multi-protein assemblies starting from subunit structural models. CombDock can assemble subunits without any assumptions about the pairwise interactions between subunits, while DockStar relies on the interaction graph or, alternatively, a homology model or a cryo-electron microscopy (EM) density map of the entire complex. We demonstrate the two methods using RNA polymerase II with 12 subunits and TRiC/CCT chaperonin with 16 subunits.

UI	MeSH Term	Description	Entries
D011506	Proteins	Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.	Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D012319	RNA Polymerase II	A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.	DNA-Dependent RNA Polymerase II,RNA Pol II,RNA Polymerase B,DNA Dependent RNA Polymerase II
D056004	Molecular Dynamics Simulation	A computer simulation developed to study the motion of molecules over a period of time.	Molecular Dynamics Simulations,Molecular Dynamics,Dynamic, Molecular,Dynamics Simulation, Molecular,Dynamics Simulations, Molecular,Dynamics, Molecular,Molecular Dynamic,Simulation, Molecular Dynamics,Simulations, Molecular Dynamics
D056404	Chaperonin Containing TCP-1	A group II chaperonin found in eukaryotic CYTOSOL. It is comprised of eight subunits with each subunit encoded by a separate gene. This chaperonin is named after one of its subunits which is a T-COMPLEX REGION-encoded polypeptide.	CCT delta Subunit,Chaperonin CCT,Chaperonin CCT, alpha Subunit,Chaperonin CCT, beta Subunit,Chaperonin CCT, delta Subunit,Chaperonin CCT, epsilon Subunit,Chaperonin CCT, eta Subunit,Chaperonin CCT, gamma Subunit,Chaperonin CCT, theta Subunit,Chaperonin CCT, zeta1 Subunit,Chaperonin CCT, zeta2 Subunit,Chaperonin Containing TCP1, Subunit 1,Chaperonin Containing TCP1, Subunit 2,Chaperonin Containing TCP1, Subunit 3,Chaperonin Containing TCP1, Subunit 4,Chaperonin Containing TCP1, Subunit 5,Chaperonin Containing TCP1, Subunit 6A,Chaperonin Containing TCP1, Subunit 6B,Chaperonin Containing TCP1, Subunit 7,Chaperonin Containing TCP1, Subunit 8,Chaperonin Containing t-Complex Polypeptide,Chaperonin-Containing T-Complex Polypeptide 1,Cytosolic Chaperonin,Cytosolic Molecular Chaperone CCT,Testis Complex Polypeptide 1,t-Complex Polypeptide 1,t-Complex Protein 1,Chaperonin Containing T Complex Polypeptide 1,Chaperonin Containing TCP 1,Chaperonin Containing t Complex Polypeptide,Chaperonin, Cytosolic,t Complex Polypeptide 1,t Complex Protein 1
D018833	Chaperonins	A family of multisubunit protein complexes that form into large cylindrical structures which bind to and encapsulate non-native proteins. Chaperonins utilize the energy of ATP hydrolysis to enhance the efficiency of PROTEIN FOLDING reactions and thereby help proteins reach their functional conformation. The family of chaperonins is split into GROUP I CHAPERONINS, and GROUP II CHAPERONINS, with each group having its own repertoire of protein subunits and subcellular preferences.	Chaperonin,Chaperonin Complex,Chaperonin Complexes,Chaperonin Family,Chaperonin Protein Complex,Complex, Chaperonin
D019295	Computational Biology	A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.	Bioinformatics,Molecular Biology, Computational,Bio-Informatics,Biology, Computational,Computational Molecular Biology,Bio Informatics,Bio-Informatic,Bioinformatic,Biologies, Computational Molecular,Biology, Computational Molecular,Computational Molecular Biologies,Molecular Biologies, Computational
D020285	Cryoelectron Microscopy	Electron microscopy involving rapid freezing of the samples. The imaging of frozen-hydrated molecules and organelles permits the best possible resolution closest to the living state, free of chemical fixatives or stains.	Electron Cryomicroscopy,Cryo-electron Microscopy,Cryo electron Microscopy,Cryo-electron Microscopies,Cryoelectron Microscopies,Cryomicroscopies, Electron,Cryomicroscopy, Electron,Electron Cryomicroscopies,Microscopies, Cryo-electron,Microscopies, Cryoelectron,Microscopy, Cryo-electron,Microscopy, Cryoelectron
D021122	Protein Subunits	Single chains of amino acids that are the units of multimeric PROTEINS. Multimeric proteins can be composed of identical or non-identical subunits. One or more monomeric subunits may compose a protomer which itself is a subunit structure of a larger assembly.	Protomers,Protein Subunit,Protomer,Subunit, Protein,Subunits, Protein