R. L. Gonzalez

Increasing the accuracy of single-molecule data analysis using tMAVEN

This paper introduces tMAVEN, a software platform for analyzing single-molecule data using multiple kinetic models to improve accuracy by addressing mismatches between models and molecular mechanisms.

The eIF3a subunit drives RNA binding within the eIF3 complex

This study reconstitutes a biochemically active yeast eIF3 complex and shows that eIF3a provides core RNA-binding activity, modulated by interactions with other subunits.

The mechanism of mRNA activation

This study uses single-molecule fluorescence imaging to investigate how eIF4F recognizes and activates mRNA caps, revealing allosteric communication and subunit functions in the process.

Cryo-EM studies of the four E. coli paralogs establish ABCF proteins as master plumbers of the peptidyl-transferase center of the ribosome

This study presents cryo-EM structures of four E. coli ABCF paralogs bound to the ribosome, revealing their role in modulating tRNA geometry and catalytic function at the peptidyl-transferase center.

Comparative genetic, biochemical, and biophysical analyses of the four E. coli ABCF paralogs support distinct functions related to mRNA translation

The paper compares four E. coli ABCF paralogs to determine their distinct roles in mRNA translation using biochemical and biophysical assays.

Mechanistic implications of the interaction of the soluble substrate-binding protein with a type II ABC importer

The paper investigates the interaction kinetics of the SBP with a type II ABC importer using FRET, revealing a locked complex formation that requires ATP hydrolysis and is inhibited by ATP or B12 binding.

Realtime observation of ATP-driven single B12 molecule translocationthrough BtuCD-F

This study uses smFRET to observe real-time ATP-driven translocation of B12 through the E. coli BtuCD-F transporter, revealing two sequential conformational changes.

Entropic control of the free energy landscape of an archetypal biomolecular machine

This study reveals how ligands modulate the free energy landscape of the bacterial ribosome by altering its structural flexibility, suggesting entropic control as a general mechanism for regulating biomolecular machines.

Elevator mechanism dynamics in a sodium-coupled dicarboxylate transporter

This study uses single-molecule experiments to show that VcINDY, a sodium-coupled dicarboxylate transporter, uses stochastic elevator-like motions for substrate translocation, with non-cooperative protomer movements and cooperative binding.

Characterizing the conformational free-energy landscape of RNA stem-loops using single-molecule field-effect transistors

This study uses single-molecule field-effect transistors to analyze the conformational free-energy landscape of RNA stem-loops, revealing a rugged landscape with unfolding timescales of 1-200 ms.

NusG links transcription and translation in Escherichia coli extracts

This study develops an in vitro system to investigate NusG's role in transcription-translation coupling in E. coli and shows NusG enhances gene expression by preventing RNAP backtracking.

Mechanistic studies of non-canonical amino acid mutagenesis

This paper describes biochemical and single-molecule assays to study the mechanisms of non-canonical amino acid incorporation into peptides and guide engineering efforts.

Insights into Genome Recoding from the Mechanism of a Classic +1-Frameshifting tRNA

This study elucidates the mechanism of +1-frameshifting by tRNA SufB2, showing it uses triplet-slippage and ribosome conformational changes to decode quadruplet codons for genome recoding.

Bayesian inference: The comprehensive approach to analyzing single-molecule experiments

The paper explains how Bayesian inference provides a comprehensive framework for analyzing single-molecule experiments by rigorously accounting for uncertainties and integrating multiple experiments.

Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing

The paper reports ribosome structures with tRNAPro bound to codons, showing how m1G37 modification prevents frameshifting by stabilizing tRNA interactions.

Elongation Inhibitors do not Prevent the Release of Puromycylated Nascent Polypeptide Chains from Ribosomes

This study shows that elongation inhibitors do not prevent the release of puromycylated nascent polypeptides from ribosomes, challenging the use of anti-puromycin staining to determine translation sites.

5' UTR recruitment of eIF4GI or DAP5 drives cap-independent translation for a subset of human mRNAs

The paper identifies that eIF4GI and DAP5 bind to 5' UTRs of specific mRNAs, enabling cap-independent translation under stress conditions.

(p)ppGpp directly regulates translation initiation during entry into quiescence

This study shows that (p)ppGpp inhibits protein synthesis in Bacillus subtilis during quiescence by targeting the GTPase IF2, preventing its allosteric activation during translation initiation.

Multiplexed, bioorthogonal labeling of multicomponent, biomolecular complexes using genomically encoded, non-canonical amino acids

The paper develops a method to label multicomponent biomolecular complexes with non-canonical amino acids for structural analysis, demonstrating its use in studying ribosome dynamics with smFRET.

Bayesian-estimated hierarchical HMMs enable robust analysis of single-molecule kinetic heterogeneity

This paper introduces hFRET, a computational tool using Bayesian hierarchical HMMs to analyze single-molecule kinetic heterogeneity, demonstrating its effectiveness with simulated and experimental data.

D-amino acid-mediated translation arrest is modulated by the identity of the incoming aminoacyl-tRNA

This study shows that the identity of both the D-aminoacyl-tRNA donor and the aminoacyl-tRNA acceptor determines ribosomal translation arrest through PTC inactivation.

Increasing the time resolution of single-molecule experiments with Bayesian inference

This paper introduces a Bayesian inference method to enhance time resolution in single-molecule experiments by inferring faster dynamics than the experimental technique can capture.