Biology subjects

Lopez, K. E.

Publications and source records attributed to Lopez, K. E..

5 recordsLinked to original sources

bioRxiv2026

Albumin integrates liver functional status to initiate regeneration

How an organism detects organ injury to initiate regeneration remains one of the central unresolved questions in regenerative biology. The liver is the only solid organ in mammals capable of complete regeneration, a process initiated by hepatocyte growth factor (Hgf) upregulation, yet the mechanism linking liver injury to Hgf induction has been unknown. Here we identify an albumin-based sensing mechanism that continuously reports the livers functional status to hepatic stellate cells to gate the regenerative program. Using single-molecule RNA FISH, parabiosis, and an ex vivo plasma assay, we show that stellate cells are the predominant source of Hgf and that a circulating, protein-dependent signal suppresses Hgf expression when the liver is functional. Biochemical fractionation, immunodepletion, and albumin knockout mice together demonstrate that this suppressive signal is a molecule carried by albumin rather than albumin itself. Untargeted metabolomics identified retinol as the albumin-associated suppressive molecule, which we confirm is sufficient to restore Hgf suppression in injured liver plasma. Conversely, long-chain fatty acids that rise after hepatectomy, specifically palmitate and linoleate, which compete for the same albumin binding site, are sufficient to derepress Hgf in healthy plasma. These data support a dual-input model in which albumin functions as an AND gate, integrating retinol loss and fatty acid gain as coincident indicators of liver injury before permitting Hgf derepression. Consistent with this model, acute in vivo knockdown of albumin is sufficient to derepress Hgf in stellate cells and drive liver overgrowth. These findings establish albumin as an active integrator of physiological signals that governs tissue-scale regenerative decisions and reveal that the liver is constitutively poised to regenerate, gatekept by signals that directly reflect its own functional status.

physiology↗

bioRxiv2026

TRPV1 antagonism occurs through diverse structural mechanisms

Transient receptor potential vanilloid 1 (TRPV1) ion channel mediates thermosensation and pain and is a target for non-addictive analgesics; however, clinical candidates have failed due to thermoregulatory side effects. Limited structural data for human TRPV1 (hTRPV1) bound to clinically relevant antagonists has constrained mechanistic insight. Using chemoinformatics-informed cryo-EM and BRET assays, we define the structural basis of antagonism across diverse chemotypes, including failed clinical compounds. A structure of hTRPV1 bound to 6-iodo-dihydrocapsaicin shows how a single substitution converts an agonist into an antagonist. Additional structures with Asivatrep, Mavatrep, and JNJ-17203212 reveal vanilloid pocket plasticity and divergent interaction networks, including lipid co-binding. Despite this diversity, antagonists converge on a conserved inhibited state, showing high potency is maintained across flexible binding modes. These findings redefine our understanding of hTRPV1 antagonism and illustrate how chemically diverse ligands stabilize an inhibited state in polymodal ion channels, laying groundwork for next-generation analgesics with improved safety.

biophysics↗

bioRxiv2021

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.

biophysics↗

bioRxiv2020

Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding

Protein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteins in vivo remains largely uncharacterized, in part due to the challenge of probing protein structures in living cells. Here, we use deep mutational scanning to investigate how a toxic conformation of -synuclein, a dynamic protein linked to Parkinsons disease, responds to perturbations of cellular proteostasis. In the context of a course for graduate students in the UCSF Integrative Program in Quantitative Biology, we screened a comprehensive library of -synuclein missense mutants in yeast cells treated with a variety of small molecules that perturb cellular processes linked to -synuclein biology and pathobiology. We found that the conformation of -synuclein previously shown to drive yeast toxicity--an extended, membrane-bound helix--is largely unaffected by these chemical perturbations, underscoring the importance of this conformational state as a driver of cellular toxicity. On the other hand, the chemical perturbations have a significant effect on the ability of mutations to suppress -synuclein toxicity. Moreover, we find that sequence determinants of -synuclein toxicity are well described by a simple structural model of the membrane-bound helix. This model predicts that -synuclein penetrates the membrane to constant depth across its length but that membrane affinity decreases toward the C terminus, which is consistent with orthogonal biophysical measurements. Finally, we discuss how parallelized chemical genetics experiments can provide a robust framework for inquiry-based graduate coursework.

biochemistry↗

bioRxiv2019

Conformational Plasticity of the ClpAP AAA+ Protease Couples Protein Unfolding and Proteolysis

The ClpAP complex functions as a \"bacterial proteasome\" that simultaneously unfolds and degrades proteins targeted for destruction. ClpA utilizes two AAA+ domains per protomer to power substrate unfolding and translocation into the ClpP proteolytic chamber. To understand this mechanism, we determined high-resolution structures of wildtype E. coli ClpAP in distinct substrate-bound states. ClpA forms a spiral with substrate contacts across both AAA+ domains, while protomers at the seam undergo nucleotide-specific rearrangements indicating a conserved rotary mechanism. ClpA IGL loops extend flexibly to bind the planar, heptameric ClpP surface and support a large ClpA-P rotation that re-orients the translocation channel. The symmetry mismatch is maintained at the spiral seam through bind and release states of the IGL loops, which appear precisely coupled to substrate translocation. Thus, ClpA rotates around the apical surface of ClpP to processively translocate substrate into the protease.

biophysics↗