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Principal Investigator: Anna Katherine Hatstat
Organization: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
Fiscal Year: 2024
Award: $58,813
Funding agency: National Institute of General Medical Sciences
Project Summary/Abstract
Living cells have evolved intricate mechanisms to detect their environment and transduce signals across
biological membranes, inducing responses in organismal behavior. Despite the prevalence of these receptors,
our understanding of the discrete mechanisms by which signals are propagated across membranes is still
evolving. In this area, histidine kinases (HKs) are a predominant class of membrane receptors in bacteria, fungi,
and plants that regulate growth, survival, or pathogenicity. HKs sense diverse extracellular stimuli and transduce
a signal across the membrane and through multiple subdomains, activating a phosphorylation cascade and
inducing a transcriptional response. Early models proposed that HKs do so through large, rigid body shifts after
sensing extracellular stimuli. Subsequent work indicates that signals are passed between HK subdomains in a
step-wise manner, often through changes in protein dynamics, informing the hypothesis that signal transduction
is the result of thermodynamic coupling between subdomains of the HK complex. This further implies that many
conformations may be adopted in the course of HK signaling. To investigate the molecular and biophysical basis
of HK specificity and signal transduction, we propose a structure and protein design approach to interrogate
energetic thresholds, sensor specificity, and conformational bias in transmembrane signaling. First, rational and
de novo design will be used to generate non-native, thermodynamically tunable sensor domains to determine
what ligand-induced energetic response is sufficient to initiate signaling. This will be complemented with
experimental characterization of synthetic, orthogonal sensor domains identified through a sequence- and
structure-guided neural network algorithm. In parallel, we will pursue X-ray crystallography and cryo-electron
microscopy to elucidate the structure of HK complexes or isolated subdomains in various signaling states, to
inform assembly of structure-conformation-function relationships. This research will significantly advance our
understanding of energetics and dynamics in transmembrane signal transduction while advancing our ability to
use protein design and computational biology to interrogate and engineer complex biophysical mechanisms. The
proposed efforts will also directly fulfill the training goals of my postdoctoral tenure, affording the necessary skills
to prepare me for an independent research career studying and engineering signal transduction mechanisms.
Terms: <Address><Adopted><Algorithms><Area><Assay><Bacteria><Behavior><Binding><Bioassay><Biochemical><Biological><Biological Assay><Biophysical Process><Biophysics><Cell Body><Cell Communication and Signaling><Cell Signaling><Cells><Chimera><Chimera organism><Collaborations><Complex><Computational Biology><Coupling><Cryo-electron Microscopy><Cryoelectron Microscopy><Data><Data Collection><Electron Cryomicroscopy><Engineering><Environment><Exhibits><Fingerprint><Gene Transcription><Generalized Growth><Genetic Transcription><Goals><Growth><In Vitro><Intracellular Communication and Signaling><Knowledge><Libraries><Ligand Binding><Ligands><Machine Learning><Membrane><Membrane Protein Gene><Membrane Proteins><Membrane-Associated Proteins><Modeling><Molecular><Molecular Configuration><Molecular Conformation><Molecular Interaction><Molecular Stereochemistry><Mutate><Output><Pathogenicity><Pathway interactions><Phosphorylation><Plants><Postdoc><Postdoctoral Fellow><Preparation><Prevalence><Process><Protein Dynamics><Protein Engineering><Protein Phosphorylation><Proteins><RNA Expression><Receptor Protein><Receptor Signaling><Research><Research Associate><Signal Transduction><Signal Transduction Induction><Signal Transduction Systems><Signaling><Single Crystal Diffraction><Specificity><Stimulus><Structure><Structure-Activity Relationship><Surface Proteins><System><Testing><Thermodynamic><Thermodynamics><Tissue Growth><Training><Transcription><Translating><Universities><Work><X Ray Crystallographies><X-Ray Crystallography><X-Ray Diffraction Crystallography><X-Ray/Neutron Crystallography><Xray Crystallography><adversarial neural network><biologic><biological signal transduction><biological systems><biophysical foundation><biophysical mechanism><biophysical principles><biophysical sciences><career><chemical structure function><chimeras><computer biology><conformation><conformational><conformational state><conformationally><conformations><conformer><cryo-EM><cryoEM><cryogenic electron microscopy><data modeling><design><designing><extracellular><fitness><fungus><generative adversarial network><generative neural network><genetic protein engineering><histidine kinase><insight><interest><machine based learning><membrane structure><mimetics><model of data><model the data><modeling of the data><neural network algorithm><non-Native><nonnative><ontogeny><particle><pathway><post-doc><post-doctoral><post-doctoral trainee><post-doctoral training><postdoctoral training><preparations><protein design><protein structure><protein structures><protein-histidine kinase><proteins structure><receptor><reconstitute><reconstitution><research associates><response><scaffold><scaffolding><sensor><sensor histidine kinase><skills><structural biology><structure function relationship>