A5046496562- Protein Structure and Dynamics
- Enzyme Structure and Function
- Computational Drug Discovery Methods
- Mitochondrial Function and Pathology
- Bioinformatics and Genomic Networks
- Adipose Tissue and Metabolism
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Diet and metabolism studies
- Coenzyme Q10 studies and effects
- ATP Synthase and ATPases Research
- Metabolomics and Mass Spectrometry Studies
- Clostridium difficile and Clostridium perfringens research
- Toxin Mechanisms and Immunotoxins
- Veterinary medicine and infectious diseases
- Birth, Development, and Health
- Analytical Chemistry and Chromatography
- Seed Germination and Physiology
- Plant Parasitism and Resistance
- Endoplasmic Reticulum Stress and Disease
- Lipid metabolism and disorders
- Erythrocyte Function and Pathophysiology
- RNA Research and Splicing
- Allelopathy and phytotoxic interactions
- Molecular spectroscopy and chirality
University of Wisconsin–Madison
2014-2018
University of Nebraska–Lincoln
2007-2014
Kelly Services (United States)
2010
Peak-picking Of Noe Data Enabled by Restriction Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727–1728. doi: 10.1093/bioinformatics/btr200 , 2011) and includes improved features for structure calculation refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Client, Analyzer. takes as input protein sequence, a list assigned chemical shifts, nuclear Overhauser data sets (13C- and/or 15N-NOESY). The...
Pancreatic cancer has a dismal 5 year survival rate of 5.5% that not been improved over the past 25 years despite an enormous amount effort. Thus, there is urgent need to identify truly novel yet druggable protein targets for drug discovery. The human DnaJ homologue subfamily A member 1 (DNAJA1) was previously shown be downregulated 5-fold in pancreatic cells and targeted as biomarker cancer, but little known about specific biological function DNAJA1 or other members family encoded genome....
We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics simulated annealing. The protein sequence, chemical shift assignments, spectra are only required inputs. Distance constraints generated automatically ambiguously assigned peaks validated during structure...
Structure-based drug discovery requires the iterative determination of protein−ligand costructures in order to improve binding affinity and selectivity potential candidates. In general, X-ray NMR structure methods are time consuming typically limiting factor process. The application molecular docking simulations filter evaluate candidates has become a common method throughput efficiency structure-based design. Unfortunately, suffer from problems that include ambiguous ligand conformers or...
NMR ligand affinity screening is a powerful technique that routinely used in drug discovery or functional genomics to directly detect protein-ligand binding events. Binding events can be identified by monitoring differences the 1D (1)H spectrum of compound with and without protein. Although single collected within short period (2-10 min per sample), one-by-one protein against library hundreds thousands compounds requires large amount spectrometer time quantity Therefore, are usually...
The proliferation of biological databases and the easy access enabled by Internet is having a beneficial impact on sciences transforming way research conducted. There are ∼1100 molecular biology dispersed throughout Internet. To assist in functional, structural evolutionary analysis abundant number novel proteins continually identified from whole-genome sequencing, we introduce PROFESS (PROtein Function, Evolution, Structure Sequence) database. Our database designed to be versatile...
A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million are encoded prokaryotic and eukaryotic genomes, where ~30% explicitly annotated as "hypothetical" or "uncharacterized" protein. Our Comparison Protein Active-Site Structures (CPASS v.2) software compares sequence structural characteristics experimentally determined ligand binding sites to infer a functional relationship absence global structure similarity. CPASS is an important component...
The solution structure of the Bacillus subtilis protein YndB has been solved using NMR to investigate proposed biological functions. exhibits helix-grip fold, which consists a β-sheet with two small and one long α-helix, forming hydrophobic cavity that preferentially binds lipid-like molecules. Sequence comparisons proteins from eukaryotes, prokaryotes, archaea suggest is very similar eukaryote Aha1, middle domain Hsp90 induces ATPase activity. On basis these similarities, classified as...
We report that proteins with the same function bind set of small molecules from a standardized chemical library. This observation led to quantifiable and rapidly adaptable method for protein functional analysis using experimentally derived ligand binding profiles. Ligand is measured high-throughput NMR affinity screen structurally diverse The was demonstrated 19 range functions. A statistically significant similarity in profiles only observed between two functionally identical albumins five...
Abstract The bacterial genus Corynebacteria contains several pathogenic species that cause diseases such as diphtheria in humans and “cheesy gland” goats sheep. Thus, identifying new therapeutic targets to treat infections is both medically economically important. CG2496, a functionally uncharacterized protein from Corynebacterium glutamicum , was evaluated using an NMR ligand‐affinity screen. A total of 11 compounds library 460 biologically active were shown selectively bind CG2496 highly...
Summary Human COQ8A (ADCK3) and Saccharomyces cerevisiae Coq8p (collectively COQ8) are UbiB family proteins essential for mitochondrial coenzyme Q (CoQ) biosynthesis. However, the biochemical activity of COQ8 its direct role in CoQ production remain unclear, part due to lack known endogenous regulators function effective small molecules probing vivo . Here we demonstrate that possesses evolutionarily conserved ATPase is activated by binding membranes containing cardiolipin phenolic compounds...