2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
April 2nd, 2025
Version: 2
Columbia University
biophysics
biorxiv

Site-resolved energetic information from HX/MS experiments

Lu, C.Open in Google Scholar•Wells, M. L.Open in Google Scholar•Reckers, A.Open in Google Scholar•Glasgow, A.Open in Google Scholar

High-resolution energetic information about protein conformational ensembles is essential for understanding protein function, yet remains challenging to obtain. We present PIGEON-FEATHER, a method for calculating ensemble free energies of opening ({Delta}Gop) at single- or near-single-amino acid resolution for proteins of all sizes from hydrogen exchange/mass spectrometry (HX/MS) data. PIGEON-FEATHER disambiguates and reconstructs all experimentally measured HX/MS isotopic mass envelopes using a Bayesian Monte Carlo sampling approach. We applied PIGEON-FEATHER to reveal how E. coli and human dihydrofolate reductases (ecDHFR, hDHFR) have evolved distinct ensembles. We show how two competitive inhibitors bind these orthologs differently, solving the longstanding mystery of why both therapeutic molecules inhibit hDHFR, but only one inhibits ecDHFR. Extending PIGEON-FEATHER to a large protein-DNA complex, we mapped ligand-induced ensemble reweighting in the E. coli lac repressor to describe the functional switching mechanism crucial for transcriptional regulation.

Similar Papers

biorxiv
Thu Apr 03 2025
Trikafta rescues F508del-CFTR by tightening specific phosphorylation-dependent interdomain interactions
Trikafta is well-known for correcting thermal and gating defects caused by the most common cystic fibrosis mutation F508del in the human cystic fibrosis transmembrane conductance regulator even at a physiological temperature. However, the exact correction pathway is still unclear. Here, noncovalent interactions among two transmembrane domains (TMD1 and TMD2), the regulatory (R) domain and two nucl...
Wang, G.
biorxiv
Thu Apr 03 2025
Caveolin assemblies displace one bilayer leaflet to organize and bend membranes
Caveolin is a monotopic integral membrane protein, widely expressed in metazoa and responsible for constructing enigmatic membrane invaginations known as caveolae. Recently, the high-resolution structure of a purified human caveolin assembly, the CAV1-8S complex, revealed a unique organization of 11 protomers arranged in a tightly packed, radially symmetric spiral disc. One face and the outer rim ...
Doktorova, M.
•
Daum, S.
•
Reagle, T. R.
•
Cannon, H. I.
...•
Levental, I.
biorxiv
Thu Apr 03 2025
Apusomonad rhodopsins, a new family of ultraviolet to blue light absorbing rhodopsin channels
Apusomonads are a clade of understudied sediment-dwelling bacterivorous protists sister to Opisthokonta. Recently, apusomonads have been found to show a negative phototactic response to blue light. Here, by screening available apusomonad 'omics data we found genes of a distinct group of microbial rhodopsins, the ApuRs. ApuRs heterologously expressed in mammalian cells absorbed near-UV/violet or bl...
Galindo, L. J.
•
Takaramoto, S.
•
Nagata, T.
•
Rozenberg, A.
...•
Inoue, K.
biorxiv
Thu Apr 03 2025
Molecular Crowding Suppresses Mechanical Stress-Driven DNA Strand Separation
Molecular crowding influences DNA mechanics and DNA - protein interactions and is ubiquitous in living cells. Quantifying the effects of molecular crowding on DNA supercoiling is essential to relating in-vitro experiments to in-vivo DNA supercoiling. We use single molecule magnetic tweezers to study DNA supercoiling in the presence of dehydrating or crowding co-solutes. To study DNA supercoiling, ...
Desai, P. R.
•
Marko, J. F.
biorxiv
Thu Apr 03 2025
Quantifying acyl chain interdigitation in simulated bilayers via direct transbilayer interactions
In a lipid bilayer, the interactions between lipid hydrocarbon chains from opposing leaflets can influence membrane properties. These interactions include the phenomenon of interdigitation, in which an acyl chain of one leaflet extends past the bilayer midplane and into the opposing leaflet. While static interdigitation is well understood in gel phase bilayers from X-ray diffraction measurements, ...
Chaisson, E. H.
•
Heberle, F. A.
•
Doktorova, M.
biorxiv
Thu Apr 03 2025
Mechanistic basis for non-exponential bacterial growth
Bacterial populations typically exhibit exponential growth under resource-rich conditions, yet individual cells often deviate from this pattern. Recent work has shown that the elongation rates of Escherichia coli and Caulobacter crescentus increase throughout the cell cycle (super-exponential growth), while Bacillus subtilis displays a mid-cycle minimum (convex growth), and Mycobacterium tuberculo...
Cylke, A.
•
Banerjee, S.
biorxiv
Thu Apr 03 2025
Large extracellular vesicles subsets and contents discrimination: the potential of morpho mechanical approaches at single EV level
Extracellular vesicles are heterogenous lipid bound membranous structures released by different cells, showing a great potential to be used as biomarkers. They have been explored by the researchers for their role in the context of environmental toxicity. When exposed to pollutants like polycyclic aromatic hydrocarbons, they undergo surface modification as well as the change of contents in their ca...
Raizada, G.
•
Brunel, B.
•
Guillouzouic, J.
•
Le Ferrec, E.
...•
Elie-Caille, C.
biorxiv
Wed Apr 02 2025
Generative Landscapes and Dynamics to Design Multidomain Artificial Transmembrane Transporters
Protein design is challenging as it requires simultaneous consideration of interconnected factors, such as fold, dynamics, and function. These evolutionary constraints are encoded in protein sequences and can be learned through the latent generative landscape (LGL) framework to predict functional sequences by leveraging evolutionary patterns, enabling exploration of uncharted sequence space. By si...
Ortega, F. M.
•
Hossain, F.
•
Volobouev, V. V.
•
Meloni, G.
...•
Morcos, F.
biorxiv
Wed Apr 02 2025
Flow Currents Support Simple and Versatile Trail-Tracking Strategies
Aquatic animals offer compelling evidence that flow sensing alone, without vision, is sufficient to guide a swimming organism to the source of an unsteady hydrodynamic trail. However, the sensory feedback strategies that allow these remarkable trail tracking abilities remain opaque. Here, by integrating mechanistic flow simulations with reinforcement learning techniques, we discovered two simple a...
Hang, H.
•
Jiao, Y.
•
Merel, J.
•
Kanso, E.