title: On the Use of low-resolution Data to Improve Structure Prediction of Proteins and Protein Complexes.
abstract: We present a systematic study of the ability of low-resolution experimental data, when combined with physical/statistical scoring functions, to improve the quality of theoretical structural models of proteins and protein complexes. Particularly, we have analyzed in detail the "extra value" added to the theoretical models by: electrospray mass spectrometry (ESI-MS), small-angle X-ray scattering (SAXS), and hydrodynamic measurements. We found that any low-resolution structural data, even when (as in the case of mass spectrometry) obtained in conditions far from the physiological ones, help to improve the quality of theoretical models, but not all the coarse-grained experimental results are equally rich in information. The best results are always obtained when using SAXS data as experimental constraints, but either hydrodynamics or gas phase CCS data contribute to improving model prediction. The combination of suitable scoring functions and broadly available low-resolution structural data (technically easier to obtain) yields structural models that are notably close to the real structures.
authors.affiliation: Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona 08028, Spain, and National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Marco
authors.initials: M
authors.lastname: D'Abramo
authors.affiliation: Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona 08028, Spain, and National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Tim
authors.initials: T
authors.lastname: Meyer
authors.affiliation: Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona 08028, Spain, and National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Pau
authors.initials: P
authors.lastname: Bernadó
authors.affiliation: Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona 08028, Spain, and National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Carles
authors.initials: C
authors.lastname: Pons
authors.affiliation: Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona 08028, Spain, and National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Juan Fernández
authors.initials: JF
authors.lastname: Recio
authors.affiliation: Molecular Modeling and Bioinformatics Unit, IRB-BSC Joint Research Program in Computational Biology, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain and Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Structural and Computational Biology Program, Institute for Research in Biomedicine Josep Samitier 1-5, Barcelona 08028, Spain, Life Sciences Department, Barcelona Supercomputing Center, Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Avgda Diagonal 645, Barcelona 08028, Spain, and National Institute of Bioinformatics, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco