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Our Science – Wang Website

Yun-Xing Wang, Ph.D.

Selected Links
•  The 3P program package - “3Pâ€� stands for periodicity, planarity, and pixel. The 3P program is based on the intrinsic periodic correlations between residual dipolar couplings (RDCs) and in-plane internuclear vectors, and between RDCs and the orientation of peptide planes relative to an alignment tensor. The program extracts accurate rhombic, axial components of the alignment tensor without explicit coordinates, and discrete peptide plane orientations, which are utilized in combination with readily available phi/psi angles to determine the three-dimensional backbone structures of proteins. The 3P program uses one alignment tensor. The package includes the detailed examples that demonstrate the utility and robustness of the program, using both experimental and synthetic data sets, which were added with different levels of noise or were incomplete. The output of the program is interfaced to Xplor-NIH.
•  Refining protein structures with the Small Angle Neutron Scattering data and NMR restraints (1) - While the restraints of residual dipolar couplings (RDCs) define the relative orientations among domains of multi-domain proteins, the relative positioning among the domains is under-defined, when few inter-domain NOE-distance restraints are available. Since the Small Angle X-ray/Neutron Scattering data contains the information about the global shape of a protein, we developed a protocol to refine protein structures with the restraint of the Small Angle Neutron Scattering (SANS) data, in addition to distance, dihedral and RDC restraints. This protocol is demonstrated in determining the structure of ribosome protein L11 [Lee, D.et al. The Structure of Free L11 and Functional Dynamics of L11 in Free, L11-rRNA(58 nt) Binary and L11-rRNA(58 nt)-thiostrepton Ternary Complexes. J. Mol. Biol., 367(4), 1007-1022, 2007.]. This link contains the Xplor-nih protocol that used for the refinement calculation.
•  Refining protein structures with the Small Angle Neutron Scattering data and NMR restraints (2) - Receptor associated protein RAP consists of three domains that are connected by two long and flexible linkers. There is no detectable interactions among the domains. The question to ask is what is the overall structure of RAP, if there is any. In order to answer this question, we utilized SANS to refine the structure of RAP. Since the linkers among the domains are flexible and there is no detectable interaction among the domains, we expect the co-existence of multi-conformers in solution and the scattering data, SAXS and SANS, are ideal to characterize the conformation space of RAP in solution. We developed a protocol to refine multi-ensembles of structures against experimental SANS data. We found that three ensembles gave the best Chi^2 in terms of fitting to the experimental SANS curve of RAP. One can find the download of the protocol from the link.
•  Define interface in a homodimeric RNA:RNA complex and refine the global structure - to be addded

This page was last updated on 7/21/2008.