A5032679646- Bioinformatics and Genomic Networks
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Bacterial Genetics and Biotechnology
- Escherichia coli research studies
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Antibiotics Pharmacokinetics and Efficacy
- RNA modifications and cancer
- Antibiotic Resistance in Bacteria
- Biotin and Related Studies
- Bacillus and Francisella bacterial research
- Natural Language Processing Techniques
- Machine Learning in Bioinformatics
- Pneumonia and Respiratory Infections
- Yersinia bacterium, plague, ectoparasites research
- Enzyme Structure and Function
- Clostridium difficile and Clostridium perfringens research
- Microbial Natural Products and Biosynthesis
University of Notre Dame
2013-2020
University of Oklahoma
2016
Anfinsen's principle asserts that all information required to specify the structure of a protein is encoded in its amino acid sequence. However, during synthesis by ribosome, N-terminus nascent chain can begin fold before C-terminus available. We tested whether this cotranslational folding alter folded an vivo, versus formed when refolded vitro. designed fluorescent consisting three half-domains, where N- and C-terminal half-domains compete with each other interact central half-domain. The...
Antibiotic resistance is a major threat to human welfare. Inhibitors of multidrug efflux pumps (EPIs) are promising alternative therapeutics that could revive activities antibiotics and reduce bacterial virulence. Identification new druggable sites for inhibition critical the development effective EPIs, especially in light constantly emerging resistance. Here, we describe EPIs interact with periplasmic membrane fusion proteins, components responsible activation transporter recruitment...
Synonymous rare codons are considered to be sub-optimal for gene expression because they translated more slowly than common codons. Yet surprisingly, many protein coding sequences include large clusters of synonymous Rare at the 5' terminus have been shown increase translational efficiency. Although a general functional role farther within has not yet established, several recent reports identified rare-to-common codon substitutions that impair folding encoded protein. Here we test hypothesis...
Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close 3-dimensional (3D) structure, 3D contact approaches complement approaches. Traditional study structures directly and alignment-based. Instead, modeled as structure networks (PSNs). Then, network compare proteins by comparing their PSNs. These alignment-based or alignment-free. We focus on latter. Existing alignment-free have drawbacks: 1) They rely naive measures of...
Autotransporter (AT) proteins are a broad class of virulence factors from Gram-negative pathogens. AT outer membrane (OM) secretion appears simple in many regards, yet the mechanism that enables transport central 'passenger' across OM remains unclear. efficiency for two passengers is enhanced by approximately 20 kDa stable core at C-terminus passenger, but studies on broader range needed order to determine whether stability difference between passenger N- and represents truly common...
The periplasm of Gram-negative bacteria includes a variety molecular chaperones that shepherd the folding and targeting secreted proteins. A central player this quality control network is DegP, protease also suggested to have chaperone function. We serendipitously discovered production Bordetella pertussis autotransporter virulence protein pertactin lethal in Escherichia coli ΔdegP strains. investigated specific contributions DegP secretion as model system test functions vivo. activity was...
An amendment to this paper has been published and can be accessed via a link at the top of paper.
Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close 3-dimensional (3D) structure, 3D contact approaches complement approaches. Traditional study structures directly. Instead, modeled as structure networks (PSNs). Then, network compare proteins by comparing their PSNs. Network may improve upon traditional We cannot use existing PSN to test this, because: 1) They rely on naive measures of topology. 2) not robust size....