About

Loren Hough is an Associate Professor at the BioFrontiers Institute in the Department of Physics at the University of Colorado Boulder. His research focuses on the biophysics of disordered proteins and developing innovative methodologies to investigate previously uncharacterized protein domains. Hough combines physical, computational, and biological approaches to find new applications for established technology, notably using nuclear magnetic resonance (NMR) spectroscopy to study protein activity in living cells. His work has centered on tubulin, an essential scaffolding protein involved in many cellular processes, with a particular focus on the C-terminal tails of tubulin molecules. He employs a cross-disciplinary process involving bacteria and Tetrahymena to label tubulin for NMR visualization, and applies this technique to other disordered protein domains implicated in neurodegenerative diseases such as Alzheimer’s and Parkinson’s. Hough's innovative research program has garnered recognition as a Boettcher Investigator and through an NIH MIRA grant. He has established a state-of-the-art biophysics laboratory, mentors students, and actively promotes diversity within the scientific community by advising groups like CU Café and mentoring students from diverse backgrounds.

Research topics

• Physics
• Chemistry
• Biology
• Artificial Intelligence
• Biophysics
• Computer Science
• Chemical physics
• Thermodynamics
• Cell biology
• Biological system
• Computational biology
• Nanotechnology
• Crystallography
• Biochemistry
• Mathematics

Selected publications

• Tubulin C-terminal tails are pH sensors that regulate microtubule function

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-08

  articleOpen accessSenior authorCorresponding

  Abstract Changes in intracellular pH are critical for maintaining homeostasis, mediating signaling pathways, and enabling cellular responses to stress, injury, and disease. There is increasing evidence that clusters of acidic residues, primarily glutamates, are both highly prevalent and conserved in disordered regions of proteins and can play an important role in cellular pH response. Tubulin C-terminal tails (CTTs) are glutamate rich regions which protrude from the microtubule surface. These tails are a primary site of for both post-translational modifications and binding of microtubule-associated proteins. Motivated by these observations, we measured the pH response of tubulin CTTs using NMR spectroscopy, circular dichroism, and computational simulations. We find that glutamate residues in CTTs taken from organisms across eukaryotes exhibit a robust upshift in their p K a values, that the sequential context of glutamate residues creates hot spots for protonation, and that hydrogen bonding between side chains stabilizes interactions that alter the conformation of the CTT. To determine whether the CTT pH response plays a potentially important role in microtubule interactions, we measured the pH dependence of the binding of the yeast kinesin-5, Cin8, to microtubules. We find that Cin8 binding is modulated by pH in a CTT-dependent manner. Our results demonstrate that acidic clusters are important mediators of cellular pH response and establish that pH can regulate interactions at the microtubule surface. Significance Statement Variation in cellular pH is important for cell function in changing environmental conditions or developmental states. Here we probe protonation of the glutamate-rich C-terminal tails of tubulin, revealing the existence of and mechanism driving the anomalously high pH response and subsequent regulation of microtubule binding. Our results demonstrate that acidic clusters are important mediators of cellular pH response and establish pH-based regulation of interactions at the microtubule surface.

  PublisherOA PDFDOI

• BPS2026 – Uncovering the domains of pericentrin that might enable its phase-separation propensity

  Biophysical Journal · 2026-02-01

  articleSenior author
  PublisherDOI

• Missense mutations in intrinsically disordered protein regions link pathogenicity and phase separation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-24 · 1 citations

  preprintOpen access

  Abstract The impact of missense genetic variations on protein function is often enigmatic, especially for mutations that map to intrinsically disordered regions (IDRs). Given the functional importance of phase separation of IDRs, it has been proposed that mutations that modulate phase separation might preferentially lead to disease. To examine this idea, we used the robust predictability of phase-separating (PS) IDRs and annotation of disease-associated proteins and mutations to map the correlation between disease and phase separation. Consistent with previous work linking phase separation to cancer and autism spectrum disorder, we find a higher prevalence of predicted phase separation behavior in disease-associated proteins than typical for human proteins. We map the prevalence of phase separation across a wide range of diseases, finding that many, but not all, show an enrichment of phase separation in the proteins associated with them. Strikingly, the pathogenic mutation rate in predicted PS IDRs was elevated three-fold relative to IDRs not predicted to phase separate. Substitutions involving arginine and the aromatic types were among the most pathogenic for PS IDRs, while substitutions involving serine, threonine, and alanine the most benign. We applied these trends to mutations of uncertain clinical significance and predict that half found in PS IDRs are likely pathogenic. We find that phosphorylation sites were enriched in PS IDRs when compared to other protein regions, though mutations at such sites were mostly benign. Pathogenicity was highest for mutations in predicted PS IDRs when also found in a short linear motif, known mediators of protein-protein interactions.

  PublisherOA PDFDOI

• Nonspecific interactions can lead to liquid-liquid phase separation in coiled-coil proteins models

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-15

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Liquid-liquid phase separation (LLPS) is one mechanism that cells can use to organize biomolecules spatially and functionally. Some coiled-coil (CC) proteins, such as the centrosomal proteins pericentrin and spd-5, are thought to LLPS, but it is currently unknown what parts of these proteins facilitate the process. It is thought, however, that the numerous CC domains in these proteins might be contributing to their LLPS. We recently showed, using computational studies and designed proteins, that CC domains can facilitate LLPS through specific interactions between the CC domains themselves, meaning that each CC was designed to interact only with a subset of other CCs in the system. This is in contrast to nonspecific interactions, where all CCs would be able to interact with all other CCs in the system, which is akin to some interactions (e.g. π – π ) seen in phase-separating intrinsically disordered proteins. Because the specificity of interactions between natural CC domains is tunable in a sequence-dependent fashion, CC domains present a unique system that allows us to investigate the contributions of specific versus nonspecific interactions on LLPS. We show, in our computational system, that CC proteins with nonspecific interactions can LLPS but with less propensity compared to specific interactions. The LLPS propensity of CC proteins with nonspecific interactions can be improved by altering the structure and dynamics of linker segments, without directly changing the specificity of interactions. We also demonstrate that the number of intra-chain CC contacts plays a direct role in determining LLPS for nonspecifically interacting proteins. These results have broad implications for the role of linker segments—protein features beyond the interaction domains e.g. ‘stickers’—in protein LLPS and the formation of biomolecular condensates. STATEMENT OF SIGNIFICANCE Model coiled-coil proteins, which use coiled-coil domains as stickers, are capable of phase separation in a regime where intra-protein contacts interfere with the interactions which support phase separation. We explore ways to increase phase separation propensity without changing interaction specificity and find that the structure and size of spacers impacts LLPS propensity by affecting the formation of intra-chain interactions. This work demonstrates that protein LLPS might be controllable without directly affecting the cohesive parts of a protein i.e. stickers. This work also suggests that LLPS propensity might be a broadly accessible phenomenon for coiled-coil proteins.

  PublisherOA PDFDOI

• Missense mutations in intrinsically disordered protein regions link pathogenicity and phase separation

  Journal of Biological Chemistry · 2025-09-29 · 2 citations

  articleOpen access

  The impact of missense genetic variations on protein function is often enigmatic, especially for mutations that map to intrinsically disordered regions (IDRs). Given the functional importance of phase separation of IDRs, it has been proposed that mutations that modulate phase separation might preferentially lead to disease. To examine this idea, we used the robust predictability of phase-separating (PS) IDRs and annotation of disease-associated proteins and mutations to map the correlation between disease and phase separation. Consistent with previous work linking phase separation to cancer and autism spectrum disorder, we find a higher prevalence of predicted phase separation behavior in disease-associated proteins than typical for human proteins. We map the prevalence of phase separation across a wide range of diseases, finding that many, but not all, show an enrichment of phase separation in the proteins associated with them. Strikingly, the pathogenic mutation rate in predicted PS IDRs was elevated threefold relative to IDRs not predicted to phase separate. Substitutions involving arginine and the aromatic types were among the most pathogenic for PS IDRs, whereas substitutions involving serine, threonine, and alanine were the most benign. We applied these trends to mutations of uncertain clinical significance and predict that half found in PS IDRs are likely pathogenic. We find that phosphorylation sites were enriched in PS IDRs when compared with other protein regions, though mutations at such sites were mostly benign. Pathogenicity was highest for mutations in predicted PS IDRs when also found in a short linear motif, known mediators of protein-protein interactions.

  PublisherDOI

• Nonspecific interactions can lead to liquid-liquid phase separation in coiled-coil protein models

  Biophysical Journal · 2025-11-21 · 1 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• BPS2025 - Liquid-liquid phase separation propensity of coiled-coil proteins revealed by molecular simulation

  Biophysical Journal · 2025-02-01

  articleOpen access
  PublisherOA PDFDOI

• BPS2025 - pH response of intrinsically disordered regions

  Biophysical Journal · 2025-02-01

  articleSenior author
  PublisherDOI

• Tubulin C-terminal tail regulation by intracellular pH

  Biophysical Journal · 2024-02-01

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Biophysical characterization of high-confidence, small human proteins

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-04-15 · 2 citations

  preprintOpen accessSenior authorCorresponding

  Significant efforts have been made to characterize the biophysical properties of proteins. Small proteins have received less attention because their annotation has historically been less reliable. However, recent improvements in sequencing, proteomics, and bioinformatics techniques have led to the high-confidence annotation of small open reading frames (smORFs) that encode for functional proteins, producing smORF-encoded proteins (SEPs). SEPs have been found to perform critical functions in several species, including humans. While significant efforts have been made to annotate SEPs, less attention has been given to the biophysical properties of these proteins. We characterized the distributions of predicted and curated biophysical properties, including sequence composition, structure, localization, function, and disease association of a conservative list of previously identified human SEPs. We found significant differences between SEPs and both larger proteins and control sets. Additionally, we provide an example of how our characterization of biophysical properties can contribute to distinguishing protein-coding smORFs from non-coding ones in otherwise ambiguous cases.

  PublisherOA PDFDOI

Recent grants

• CAREER: Molecular mechanisms underlying yeast cellular starvation tolerance; spatial reasoning to increase STEM participation

  NSF · $1.1M · 2020–2026

• NIH Grant F32GM087854

  NIH · $61k · 2011

• Molecular dissection of the C-terminal tails of tubulin and the effect of their polyglycylation on binding and microtubule assembly

  NIH · $1.8M · 2016–2022

Frequent coauthors

• Noel A. Clark

  University of Colorado Boulder

  29 shared

• Meredith D. Betterton

  University of Colorado Boulder

  26 shared

• Kathryn P. Wall

  University of Colorado Boulder

  21 shared

• Matthew A. Glaser

  University of Colorado Boulder

  20 shared

• David M. Walba

  University of Colorado Boulder

  18 shared

• Laura Maguire

  University of Colorado System

  18 shared

• Joseph E. Maclennan

  University of Colorado Boulder

  16 shared

• David Cowburn

  Albert Einstein College of Medicine

  14 shared

Education

• B.A., Physics

  Harvard

• Ph.D., Physics

  University of Colorado Boulder

Awards & honors

• Boettcher Investigator (2014)
• MIRA grant from the NIH (2016)