M. J. Harms

Navigating contradictions: Salmonella Typhimurium chemotaxis amidst conflicting stimuli of the intestinal environment

This study shows that indole in feces does not protect against Salmonella infection and may instead aid pathogen survival by attracting bacteria to low-competitor-density niches.

Bacterial vampirism mediated through taxis to serum

The paper identifies chemotaxis to human serum as a mechanism enabling Enterobacteriaceae to invade bloodstream infections, termed 'bacterial vampirism'.

The importance of input sequence set to consensus-derived proteins and their relationship to reconstructed ancestral proteins

The paper compares consensus and ancestral protein reconstruction methods using Ribonuclease H sequences, finding that phylogenetically restricted consensus proteins are more stable than those from diverse clades.

Disentangling contact and ensemble epistasis in a riboswitch

The paper investigates contact and ensemble epistasis in an RNA riboswitch by analyzing mutation effects across different allosteric effector concentrations, finding both mechanisms contribute to epistasis.

An experimental demonstration of ensemble epistasis in the lac repressor

The paper experimentally demonstrates ensemble epistasis in the lac repressor, showing that mutations alter conformational ensembles, leading to significant epistatic effects in DNA binding and gene expression.

Higher-order interactions shape microbial interactions as microbial community complexity increases

The paper investigates how microbial interactions change with community complexity, finding that higher-order interactions emerge and most conserved interactions are additive.

Evolution avoids a pathological stabilizing interaction in the immune protein S100A9

The paper identifies a mutation in S100A9 that stabilizes a non-functional conformation, revealing an evolutionary constraint on stabilizing mutations.

Ensemble epistasis: thermodynamic origins of non-additivity between mutations

The paper shows that ensemble epistasis, arising from thermodynamic ensembles in macromolecules, is a common source of non-additivity between mutations.

Exploring the evolutionary history of kinetic stability in the alpha-lytic protease family

This study investigates how sequence variation in the alpha-lytic protease family relates to kinetic stability and energy landscapes, finding that pro-region size and specific amino acids influence folding speed and stability.

Learning Peptide Recognition Rules for a Low-Specificity Protein

The paper trains a machine learning model to predict peptide binding specificity for a low-specificity protein by analyzing biochemical features rather than amino acid sequences, revealing hydrophobicity and shape complementarity as key factors.

Were ancestral proteins less specific?

The study revisits the evolution of peptide binding specificity in S100A5 and S100A6, showing that ancestral proteins have similar specificity to modern ones when measured against random peptides, challenging previous conclusions.

Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9

The paper shows how a single mutation in S100A9 affects its proinflammatory activity and proteolytic resistance while leaving S100A8/S100A9 antimicrobial activity unchanged, enabling multifunctionality in mammals.

Identification and characterization of zebrafish Tlr4 co-receptor Md-2

The paper identifies a zebrafish Md-2 homolog, ly96, and shows it forms a Tlr4a complex that activates NF-κB in response to LPS, suggesting an ancestral Tlr4/Md-2 system in vertebrates.

Zinc-independent activation of Toll-like receptor 4 by S100A9

This study shows that S100A9 can activate TLR4 without requiring Zn2+ binding, challenging previous assumptions about the role of zinc in this interaction.

Conservation of specificity in two low-specificity proteins

This study shows that low-specificity S100 proteins maintain conserved peptide binding specificity across species, indicating evolutionary constraints and subfunctionalization of paralogs.