A5068709307- Protein Structure and Dynamics
- Enzyme Structure and Function
- Advanced NMR Techniques and Applications
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Molecular spectroscopy and chirality
- Electron Spin Resonance Studies
- RNA modifications and cancer
- Spectroscopy and Quantum Chemical Studies
- Lanthanide and Transition Metal Complexes
- Glycosylation and Glycoproteins Research
- Metabolomics and Mass Spectrometry Studies
- Laser-Matter Interactions and Applications
- NMR spectroscopy and applications
- Advanced Chemical Physics Studies
- Peptidase Inhibition and Analysis
- HIV Research and Treatment
- DNA and Nucleic Acid Chemistry
- ATP Synthase and ATPases Research
- Computational Drug Discovery Methods
- Solid-state spectroscopy and crystallography
- Ubiquitin and proteasome pathways
- Advanced MRI Techniques and Applications
- HIV/AIDS drug development and treatment
- Influenza Virus Research Studies
Center for Information Technology
2014-2024
National Institutes of Health
2015-2024
National Institute of Diabetes and Digestive and Kidney Diseases
2001-2024
Foundation for the National Institutes of Health
2022-2023
Advanced Photon Source
2009
National Cancer Institute
2004-2009
University of Illinois Urbana-Champaign
2009
William & Mary
1995-2008
Williams (United States)
1995-2008
Argonne National Laboratory
2008
Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources. Here, some of Xplor-NIH's most useful data-associated energy terms are reviewed, including newer alternative options using residual dipolar coupling in calculations. Further, we discuss new developments the implementation strict symmetry calculation symmetric homo-oligomers, representation system as an ensemble structures to account motional effects....
Abstract The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation alpha-synuclein (Asyn) fibrils in bodies neurites. Here we develop validate a method to amplify Asyn extracted from LBD postmortem tissue samples use solid state nuclear magnetic resonance (SSNMR) studies determine atomic resolution structure. Amplified comprise mixture single protofilament two with very low twist. fold highly similar determined by recent cryo-electron microscopy study...
Paramagnetic relaxation enhancement (PRE) measurements on 1H nuclei have the potential to play an important role in NMR structure determination of macromolecules by providing unique long-range (10−35 Å) distance information. Recent methodological advances for covalently attaching paramagnetic groups at specific sites both proteins and nucleic acids permitted application PRE various biological macromolecules. However, because artificially introduced are exposed solvent linked macromolecule...
The magnitude of backbone internal motions in the small protein ubiquitin that needs to be invoked account for dipolar coupling data measured multiple alignment media is investigated using an intuitively straightforward approach. This involves simultaneous refinement coordinates (against NOE, torsion angle, and restraints) optimization magnitudes orientations tensors by means angle simulated annealing Cartesian space minimization. We show N−H couplings 11 different N−C', HN−C', Cα−C' two can...
The HIV-1 capsid protein plays a crucial role in viral infectivity, assembling into cone that encloses the RNA. In mature virion, N-terminal domain of forms hexameric and pentameric rings, while C-terminal homodimers connect adjacent rings to one another. Structures disulfide-linked hexamer pentamer assemblies, as well structures isolated domains, have been solved previously. dimer configuration constructs differs solution (residues 144-231) crystal 146-231) by ∼30°, it has postulated former...
Abstract Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level data, and, generally, restricted small (<30 kDa) proteins. We introduce an integrated approach that simultaneously uses EM data overcome the limits of each these methods. The enables 468 kDa large dodecameric aminopeptidase TET2 a precision accuracy below 1 Å...
The N-terminal region of the huntingtin protein, encoded by exon-1, comprises an amphiphilic domain (htt NT ), a polyglutamine (Q n ) tract, and proline-rich sequence. Polyglutamine expansion results in aggregation-prone protein responsible for Huntington’s disease. Here, we study earliest events involved oligomerization minimalistic construct, htt Q 7 , which remains largely monomeric over sufficiently long period time to permit detailed quantitative NMR analysis kinetics structure sparsely...
Abstract RNA flexibility is reflected in its heterogeneous conformation. Through direct visualization using atomic force microscopy (AFM) and the adenosylcobalamin riboswitch aptamer domain as an example, we show that a single sequence folds into conformationally architecturally structures under near-physiological solution conditions. Recapitulated 3D topological from AFM molecular surfaces reveal all conformers share same secondary structural elements. Only population-weighted cohort, not...
Backbone residual dipolar coupling (N-H, Calpha-Halpha, N-C', and Calpha-C') data collected in five different media on the B3 IgG binding domain of streptococcal protein G (GB3) have been analyzed by simultaneous refinement coordinates optimization magnitudes orientations alignment tensors using single multiple structure representations. We show, appropriate error analysis, that agreement between observed calculated couplings at level experimental uncertainty is obtained with a two-structure...
The solution structures of free Enzyme I (EI, ∼128 kDa, 575 × 2 residues), the first enzyme in bacterial phosphotransferase system, and its complex with HPr (∼146 kDa) have been solved using novel methodology that makes use prior structural knowledge (namely, dimeric EIC domain isolated EIN both complexed to HPr), combined residual dipolar coupling (RDC), small- (SAXS) wide- (WAXS) angle X-ray scattering small-angle neutron (SANS) data. calculational strategy employs conjoined rigid...
The 3 ′ untranslated region (3 UTR) of turnip crinkle virus (TCV) genomic RNA contains a cap-independent translation element (CITE), which includes ribosome-binding structural (RBSE) that participates in recruitment the large ribosomal subunit. In addition, symmetric loop RBSE plays key role coordinating incompatible processes viral and replication, require enzyme progression opposite directions on template. To understand basis for subunit intricate interplay among different parts molecule,...