Andrew I. Jewett

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We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary(More)
MOTIVATION Existing algorithms for automated protein structure alignment generate contradictory results and are difficult to interpret. An algorithm which can provide a context for interpreting the alignment and uses a simple method to characterize protein structure similarity is needed. RESULTS We describe a heuristic for limiting the search space for(More)
Chaperonins, such as the GroE complex of the bacteria Escherichia coli, assist the folding of proteins under non-permissive folding conditions by providing a cavity in which the newly translated or translocated protein can be encapsulated. Whether the chaperonin cage plays a passive role in protecting the protein from aggregation, or an active role in(More)
We explore the question of whether local effects (originating from the amino acids intrinsic secondary structure propensities) or nonlocal effects (reflecting the sequence of amino acids as a whole) play a larger role in determining the fold of globular proteins. Earlier circular dichroism studies have shown that the pattern of polar, non polar amino acids(More)
The relative folding rates of simple, single-domain proteins, proteins whose folding energy landscapes are smooth, are highly dispersed and strongly correlated with native-state topology. In contrast, the relative folding rates of small, Gō-potential lattice polymers, which also exhibit smooth energy landscapes, are poorly dispersed and insignificantly(More)
The 25-35 fragment of the Alzheimer amyloid beta (Abeta) peptide is a naturally occurring proteolytic by-product that retains the toxicity of its larger, better-known counterpart, Abeta (1-40). Soluble oligomers of the amyloid-beta peptide have been implicated in the pathogenesis of Alzheimer's disease as a primary source of neurotoxicity. These oligomers(More)
The GroEL chaperonin has the ability to behave as an unfoldase, repeatedly denaturing proteins upon binding, which in turn can free them from kinetic traps and increase their folding rates. The complex formed by GroEL+GroES+ATP can also act as an infinite dilution cage, enclosing proteins within a protective container where they can fold without danger of(More)
Recent experiments suggest that the folding of certain proteins can take place entirely within a chaperonin-like cavity. These substrate proteins experience folding rate enhancements without undergoing multiple rounds of ATP-induced binding and release from the chaperonin. Rather, they undergo only a single binding event, followed by sequestration into the(More)
FtsZ, the bacterial homologue of eukaryotic tubulin, plays a central role in cell division in nearly all bacteria and many archaea. It forms filaments under the cytoplasmic membrane at the division site where, together with other proteins it recruits, it drives peptidoglycan synthesis and constricts the cell. Despite extensive study, the arrangement of FtsZ(More)
One of the more unusual attempts by the American state to mobilize academic expertise unfolded in the late 1930s, when the United States Department of Agriculture (USDA) hired scholars in the "culture and personality" fields and philosophy to aid its efforts to promote economic, social, and cultural change in the countryside. USDA progressives also reached(More)