D. S. Marks

GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway

The paper determines the cryo-EM structure of active GPR161 bound to Gs, revealing sterol binding and its role in ciliary cAMP signaling, while showing that sterol binding is not essential for Hedgehog pathway suppression.

Protein design using structure-based residue preferences

This paper introduces a method to design functional proteins using residue preferences derived from structural data, showing high accuracy in predicting combinatorial mutation effects.

The relaxin receptor RXFP1 signals through a mechanism of autoinhibition

This study determines the cryo-EM structure of active-state RXFP1 bound to relaxin-2 and Gs protein, revealing an autoinhibition mechanism.

An in silico method to assess antibody fragment polyreactivity

The paper develops a machine learning model to assess and reduce polyreactivity in nanobody sequences, achieving high accuracy and practical application through a web server.

Mechanical gating of the auditory transduction channel TMC1 involves the fourth and sixth transmembrane helices

The paper investigates how mutations in TM4 and TM6 helices of TMC1 affect mechanical gating of auditory transduction channels in hair cells.

Coevolution of interacting proteins through non-contacting and non-specific mutations

The paper identifies enabling mutations in a bacterial toxin that tolerate antitoxin mutations, showing non-specific tolerance despite covariation primarily between contacting residues.

Rapid generation of potent antibodies by autonomous hypermutation in yeast

This paper introduces AHEAD, a yeast-based system for rapid antibody generation through autonomous hypermutation, achieving high-affinity antibodies against SARS-CoV-2 and other targets in just 2 weeks.

Protein structure from experimental evolution

This study uses laboratory evolution to infer protein structures by analyzing residue interactions from evolved sequences.

Structure and mutagenic analysis of the lipid II flippase MurJ from Escherichia coli

The paper reports the crystal structure of MurJ from E. coli, performs mutagenesis to map functional sites, and identifies co-evolved interactions supporting a rocker-switch model for lipid II transport.

Viral gain-of-function experiments uncover residues under diversifying selection in nature

The paper identifies two residues in bacteriophage λ that evolved under diversifying selection in nature, supporting host-shift evolution through experimental and genomic analysis.

Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli

The paper examines core gene evolution in E. coli, finding they accumulate more nonsynonymous mutations in lab experiments but are more conserved in nature.