Physical Sciences and Mathematics Commons^™

Predicting Residue Contacts Using Pragmatic Correlated Mutations Method: Reducing The False Positives, Petras J. Kundrotas, Emil Alexov

Publications

Background

Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the predicted 3D structures. The correlated mutations (CM) method serves as the most promising approach and it has been used to predict amino acids pairs that are distant in the primary sequence but form contacts in the native 3D structure of homologous proteins.

Results

Here we report a new implementation of the CM method with an added set of selection rules (filters). The parameters of the algorithm were optimized against fifteen high resolution crystal …

Protcom: Searchable Database Of Protein Complexes Enhanced With Domain-Domain Structures, Petras Kundrotas, Emil Alexov

Publications

The database of protein complexes (PROTCOM) is a compilation of known 3D structures of protein–protein complexes enriched with artificially created domain–domain structures using the available entries in the Protein Data Bank. The domain–domain structures are generated by parsing single chain structures into loosely connected domains and are important features of the database. The database (http://www.ces.clemson.edu/compbio/protcom) could be used for benchmarking purposes of the docking and other algorithms for predicting 3D structures of protein–protein complexes. The database can be utilized as a template database in the homology or threading methods for modeling the 3D structures of unknown protein–protein complexes. …

Electrostatic Properties Of Protein-Protein Complexes, Petras J. Kundrotas, Emil Alexov

Publications

Statistical electrostatic analysis of 37 protein-protein complexes extracted from the previously developed database of protein complexes (ProtCom, http://www.ces.clemson.edu/compbio/protcom) is presented. It is shown that small interfaces have a higher content of charged and polar groups compared to large interfaces. In a vast majority of the cases the average pK_a shifts for acidic residues induced by the complex formation are negative, indicating that complex formation stabilizes their ionizable states, whereas the histidines are predicted to destabilize the complex. The individual pK_a shifts show the same tendency since 80% of the interfacial acidic groups were found to lower their …

Observations Of Triboelectric Charging Effects On Langmuir-Type Probes In Dusty Plasma, Aroh Barjatya, C. M. Swenson

Publications

Investigation of Earth’s mesosphere using sounding rockets equipped with a myriad of instruments has been a highly active field in the last 2 decades. This paper presents data from three separate instruments: an RF impedance probe, a DC fixed bias Langmuir probe, and an electric field probe, that were flown on a mesospheric sounding rocket flight investigating the presence of charged dust within and/or around a sporadic metal layer. The combined data set indicates a case of payload surface charging, the causes of which are investigated within this paper. A generic circuit model is developed to analyze payload charging and …

Rocket And Radar Investigation Of Background Electrodynamics And Bottom-Type Scattering Layers At The Onset Of Equatorial Spread F, D. L. Hysell, M. F. Larsen, C. M. Swenson, Aroh Barjatya, Et. Al

Publications

Sounding rocket experiments were conducted during the NASA EQUIS II campaign on Kwajalein Atoll designed to elucidate the electrodynamics and layer structure of the postsunset equatorial F region ionosphere prior to the onset of equatorial spread F (ESF). Experiments took place on 7 and 15 August 2004, each comprised of the launch of an instrumented and two chemical release sounding rockets. The instrumented rockets measured plasma number density, vector electric fields, and other parameters to an apogee of about 450 km. The chemical release rockets deployed trails of trimethyl aluminum (TMA) which yielded wind profile measurements. The Altair radar was …