# positions[].organizations[].parent[].label
College of Agriculture and Life Sciences

# overview
A fundamental principle of biology is the use of chemical energy in the form of ATP to assemble, disassemble and alter macromolecular structure.  Specialized control proteins known as molecular chaperones are often responsible for this activity and have been recognized in recent years to be essential for regulating many aspects of cellular biology.  Using a variety of biophysical and biochemical techniques, the Rye lab focuses on three fundamental cellular processes that require molecular chaperones:  (1) protein folding (2) protein disaggregation and (3) vesicle trafficking.  In each of these cases, large quantities ATP are burned, resulting in molecular organization in the case of protein folding, and molecular disassembly and remodeling in the case of protein disaggregation and vesicle trafficking.  We are interested in understanding the detailed biophysical mechanisms that underpin these events.  Why are these processes so energetically expensive?  Are there any similarities in how the energy is used between these very different molecular processes?  Are there general principles of energy transduction in biology that can be gleaned by comparing these examples with other molecular machines, such as cytoskeletal motors?  Understanding how molecular chaperones control protein and membrane organization will provide key insights into not only basic cell biology, but will also illuminate aspects of many diseases that spring from aberrant protein and membrane dynamics.

# keywords[]
1.1 Normal Biological Development And Functioning

# educationAndTraining[].organization.label
University of California, Berkeley - (Berkeley, California, United States)

# educationAndTraining[].organization.label
Rice University - (Houston, Texas, United States)

# publications[].label
Clathrin coat disassembly by the yeast Hsc70/Ssa1p and auxilin/Swa2p proteins observed by single-particle burst analysis spectroscopy.

# publications[].label
The Persistent Effect of Initial Substrate Protein Conformation on Productive Folding by Groel-Groes

# publications[].label
Efficient cell delivery mediated by lipid-specific endosomal escape of supercharged branched peptides.

# publications[].label
Visualizing GroEL/ES in the act of encapsulating a folding protein.

# publications[].label
Repetitive protein unfolding by the trans ring of the GroEL-GroES chaperonin complex stimulates folding.

# publications[].label
The C-terminal tails of the bacterial chaperonin GroEL stimulate protein folding by directly altering the conformation of a substrate protein.

# publications[].label
Single particle fluorescence burst analysis of epsin induced membrane fission.

# publications[].label
GroEL actively stimulates folding of the endogenous substrate protein PepQ.

# publications[].label
Protein chain collapse modulation and folding stimulation by GroEL-ES.

# publications[].publisher
American Association for the Advancement of Science (AAAS)

# publications[].label
Fluorometric assay using dimeric dyes for double- and single-stranded DNA and RNA with picogram sensitivity.

# publications[].label
High-sensitivity two-color detection of double-stranded DNA with a confocal fluorescence gel scanner using ethidium homodimer and thiazole orange

# publications[].label
The Impact of Hidden Structure on Aggregate Disassembly by Molecular Chaperones.

# publications[].label
Role of the γ‐phosphate of ATP in triggering protein folding by GroEL–GroES: function, structure and energetics

# publications[].label
Structural basis of substrate selectivity of E. coli prolidase.

# publications[].label
[30] Picogram detection of stable dye-DNA intercalation complexes with two-color laser-excited confocal fluorescence gel scanner

# publications[].label
Stable fluorescent dye-DNA complexes in high sensitivity detection of protein-DNA interactions. Application to heat shock transcription factor.

# publications[].label
High-sensitivity capillary electrophoresis of double-stranded DNA fragments using monomeric and dimeric fluorescent intercalating dyes.

# publications[].label
GroEL-mediated protein folding: making the impossible, possible.

# publications[].label
High-sensitivity DNA detection with a laser-excited confocal fluorescence gel scanner.

# publications[].label
The reaction cycle of groe-assisted protein folding

# publications[].label
Expansion and compression of a protein folding intermediate by GroEL.

# publications[].label
Burst analysis spectroscopy: A versatile single-particle approach for studying distributions of protein aggregates and fluorescent assemblies

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Development and application of multicolor burst analysis spectroscopy.

# publications[].label
Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL.

# publications[].label
Stable dye-DNA intercalation complexes as reagents for high-sensitivity fluorescence detection.

# publications[].label
Expansion and Compression of a Protein Folding Intermediate by GroEL

# publications[].label
Application of fluorescence resonance energy transfer to the GroEL-GroES chaperonin reaction.

# publications[].label
GroEL stimulates protein folding through forced unfolding.

# publications[].label
Environment-sensitive labels in multiplex fluorescence analyses of protein-DNA complexes.

# publications[].label
Characterization of the active intermediate of a GroEL-GroES-mediated protein folding reaction.

# publications[].label
Probing the conformation of the fibronectin III1-2 domain by fluorescence resonance energy transfer.

# publications[].label
Triggering protein folding within the GroEL-GroES complex.

# publications[].label
STRUCTURE AND FUNCTION IN GroEL-MEDIATED PROTEIN FOLDING

# publications[].label
[11] Construction of single-ring and two-ring hybrid versions of bacterial chaperonin GroEL

# publications[].label
Interaction of dimeric intercalating dyes with single-stranded DNA

# publications[].label
GroEL-GroES cycling: ATP and nonnative polypeptide direct alternation of folding-active rings.

# publications[].label
Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: properties and applications

# researcherOn[].label
Mechanism of protein aggregate recognition and disassembly by molecular chaperones

# researcherOn[].awardedBy.label
National Institutes of Health - (Bethesda, Maryland, United States)

# researcherOn[].awardedBy.preferredLabel
DHHS-NIH-National Institute of General Medical Science

# researcherOn[].label
Mechanism of Protein Folding Intermediate Disaggregation By Molecular Chaperones

# researcherOn[].awardedBy.label
National Institutes of Health - (Bethesda, Maryland, United States)

# researcherOn[].label
Mechanism of membrane fission at the recycling endosome

# researcherOn[].awardedBy.label
National Institutes of Health - (Bethesda, Maryland, United States)

# researcherOn[].awardedBy.preferredLabel
DHHS-NIH-National Institute of General Medical Science

# streetAddress
Texas A&M University; Biochemistry & Biophysics; 2128 TAMU

# organizations[]
College of Agriculture and Life Sciences

# schools[]
College of Agriculture and Life Sciences

# etdChairOf[].label
Weaver, Jeremy Scott (2015-05). Enhancement of Chaperone-Mediated Protein Folding Through Substrate Protein Interactions with the Groel C-Termini. Doctoral Dissertation.

# etdChairOf[].label
Brooks, Arielle L (2015-05). Single Particle Fluorescence Burst Analysis of Membrane Fission. Master's Thesis.

# etdChairOf[].label
Shoup, Daniel Wayne (2016-05). The Impact Of Hidden Aggregate Structure On Molecular Chaperone Disaggregation Revealed By Single Particle Fluorescence Burst Analysis. Doctoral Dissertation.