Caitlin Davis, PhD
Assistant ProfessorCards
Contact Info
Chemistry
225 Prospect St., PO Box 208107
New Haven, CT 06520-8107
United States
About
Titles
Assistant Professor
Biography
Caitlin obtained her Ph.D. with Prof. Brian Dyer at Emory University in 2015. During that time, she developed and applied structurally-specific time-resolved infrared techniques to probe fast protein dynamics in vitro. From 2015-2019, Caitlin was a Center for the Physics of Living Cells Postdoctoral Fellow with Prof. Martin Gruebele at University of Illinois at Urbana-Champaign. As a postdoc, she developed an in vitro mimic of the intracellular environment on protein folding and stability, and also expanded the in-cell Fast Relaxation Imaging (FReI) technique to bimolecular reactions and whole organisms.
In 2020, Caitlin started her own lab at Yale University, where she currently investigates the mechanism and dynamics of protein and RNA interactions inside cells. To achieve this goal, her group uses a combination of time-resolved infrared and fluorescence spectral imaging at multiple scales, from in vitro to single cell to whole organism. This quantitative biophysical approach is used to address kinetic questions that require characterization in the complex, heterogenous environment of the cell. This includes phase-separated bio-condensates, pre-mRNA splicing, and "quinary" RNA interactions.
Appointments
Chemistry
Assistant ProfessorPrimary
Other Departments & Organizations
Education & Training
- Center for the Physics of Living Cells Postdoctoral Fellow
- University of Illinois at Urbana-Champaign (2019)
- PhD
- Emory University, Chemistry (2015)
- BS
- University of Michigan, Chemistry and Mathematics (2007)
Research
Overview
Quantification of the physics and chemistry of biomolecule interactions inside cells is challenging due to the complex environment, fast timescales of motions, and difficulties in controlling reactions. The unifying theme of our research is the development of new quantitative spectroscopic imaging techniques to elucidate the relationship between function and dynamics of proteins and RNA inside living cells.
Our research lies at the intersection of traditional chemistry, physics, and biology disciplines, with an emphasis on quantitative physical characterization of biological systems. Our efforts combine elements of physical chemistry (thermodynamics, kinetics, spectroscopy), molecular biology (mutation, proteins, RNA), cell biology (live-cell microscopy, mammalian cell culture, zebrafish model), and theoretical chemistry (simulations and modeling).
ORCID
0000-0003-4340-4577- View Lab Website
Davis Lab
Research at a Glance
Yale Co-Authors
Publications Timeline
Corey O'Hern, PhD
Victor Batista
Publications
2024
Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling
Liu Z, Grigas A, Sumner J, Knab E, Davis C, O'Hern C. Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling. Protein Science 2024, 33: e5219. PMID: 39548730, PMCID: PMC11568256, DOI: 10.1002/pro.5219.Peer-Reviewed Original ResearchMeSH Keywords and ConceptsConceptsForster resonance energy transferProtein structure determination techniquesCellular environmentProtein structure modelingAmino acid pairsConformational changesProteins in vivoForster resonance energy transfer studiesCrowded cellular environmentStructure determination techniquesDynamics in vivoStructures in vivoInduce conformational changesProtein structureResonance energy transferRoot-mean-square deviationAcid pairsInter-residue restraintsStructural ensemblesAmino acidsNon-physiological environmentsProteinDistance restraintsNucleic acidsAminoSimilarity Metrics for Subcellular Analysis of FRET Microscopy Videos
Burke M, Batista V, Davis C. Similarity Metrics for Subcellular Analysis of FRET Microscopy Videos. The Journal Of Physical Chemistry B 2024, 128: 8344-8354. PMID: 39186078, DOI: 10.1021/acs.jpcb.4c02859.Peer-Reviewed Original ResearchConceptsForster resonance energy transferProtein-RNA interactionsHigh-resolution microscopySubcellular localizationResonance energy transferSpecialized compartmentsSubcellular analysisMicroscopy dataCellsMolecular populationsCompartmentHigh-resolution microscopy dataMolecular environmentMicroscopy videosDynamic heterogeneityExfoliation of a metal–organic framework enabled by post-synthetic cleavage of a dipyridyl dianthracene ligand
Logelin M, Schreiber E, Mercado B, Burke M, Davis C, Bartholomew A. Exfoliation of a metal–organic framework enabled by post-synthetic cleavage of a dipyridyl dianthracene ligand. Chemical Science 2024, 15: 15198-15204. PMID: 39246333, PMCID: PMC11378025, DOI: 10.1039/d4sc03524k.Peer-Reviewed Original ResearchConceptsMetal-organic frameworksZinc metal-organic frameworkStacking axisConductive 2D metal–organic frameworksThree-dimensional MOFsTwo-dimensional (2D) metal-organic frameworksCrystals of 2D materialsStimuli-responsive ligandsSynthetic tunabilityImproved crystal growthTwo-dimensional frameworkStacking directionMacroscopic crystalsDimeric ligandsLigandChemo-sensingCrystal growthStructural analysisNanoscale applicationsDianthraceneStackExfoliationAnthraceneDipyridylIncreasing orderIdentifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling
Liu Z, Grigas A, Sumner J, Knab E, Davis C, O'Hern C. Identifying the minimal sets of distance restraints for FRET‐assisted protein structural modeling. Protein Science 2024, 33 PMID: 38800659, PMCID: PMC11118665, DOI: 10.1002/pro.5219.Peer-Reviewed Original ResearchConceptsForster resonance energy transferProtein structure determination techniquesCellular environmentProtein structure modelingAmino acid pairsConformational changesForster resonance energy transfer studiesCrowded cellular environmentStructure determination techniquesInduce conformational changesProtein structureResonance energy transferRoot-mean-square deviationAcid pairsInter-residue restraintsStructural ensemblesAmino acidsNon-physiological environmentsProteinDistance restraintsNucleic acidsAminoMD simulationsFRET pairsOrganellesOleic acid differentially affects lipid droplet storage of de novo synthesized lipids in hepatocytes and adipocytes
Castillo H, Shuster S, Tarekegn L, Davis C. Oleic acid differentially affects lipid droplet storage of de novo synthesized lipids in hepatocytes and adipocytes. Chemical Communications 2024, 60: 3138-3141. PMID: 38329230, PMCID: PMC10939124, DOI: 10.1039/d3cc04829b.Peer-Reviewed Original ResearchStability vs. environmental sensitivity: The importance of protein surface charge adaptations
Knab E, Sternke M, Barrick D, Gruebele M, Davis C. Stability vs. environmental sensitivity: The importance of protein surface charge adaptations. Biophysical Journal 2024, 123: 302a. DOI: 10.1016/j.bpj.2023.11.1874.Peer-Reviewed Original ResearchConnecting simulation and experiment of protein folding inside cells with fast relaxation imaging
Sarker R, Knab E, Davis C. Connecting simulation and experiment of protein folding inside cells with fast relaxation imaging. Biophysical Journal 2024, 123: 31a. DOI: 10.1016/j.bpj.2023.11.284.Peer-Reviewed Original ResearchOleic acid differentially affects de novo lipogenesis and global lipid levels in hepatocytes
Castillo H, Shuster S, Davis C. Oleic acid differentially affects de novo lipogenesis and global lipid levels in hepatocytes. Biophysical Journal 2024, 123: 411a. DOI: 10.1016/j.bpj.2023.11.2514.Peer-Reviewed Original ResearchTardigrade CAHS hydrogels protect proteins through concentration-dependent mechanism
Barilla M, Shuster S, Davis C. Tardigrade CAHS hydrogels protect proteins through concentration-dependent mechanism. Biophysical Journal 2024, 123: 75a-76a. DOI: 10.1016/j.bpj.2023.11.529.Peer-Reviewed Original ResearchMultispectral vibrational imaging for high resolution tracking of live cell metabolic processes
Shuster S, Castillo H, Davis C. Multispectral vibrational imaging for high resolution tracking of live cell metabolic processes. Biophysical Journal 2024, 123: 449a. DOI: 10.1016/j.bpj.2023.11.2740.Peer-Reviewed Original Research
News & Links
Media
- Motivated by diseases arising from the misregulation of proteins and RNA, our biophysical approach makes connections between molecular mechanism and cellular function through time-resolved spectral imaging at multiple scales, from in vitro to single cell to whole organism.
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Chemistry
225 Prospect St., PO Box 208107
New Haven, CT 06520-8107
United States
Chemistry
350 Edwards St.
New Haven, CT 06511
United States