Marcos M. Sotomayor

Bayesian-Steered Structure Prediction of Mechanical Biomolecules Using Twisted Diffusion

This paper introduces a Bayesian-steered diffusion method for predicting alternative conformations of mechanical biomolecules, demonstrating its ability to reproduce experimentally validated states of various proteins and DNA.

PySteMoDA: An Open Source Python Package for the Analysis of Steered Molecular Dynamics Simulations Data

PySteMoDA provides an automated tool for analyzing steered molecular dynamics simulations, improving accuracy and accessibility in computational biochemistry and biophysics.

In-Situ ssDNA Isolation from dsDNA Sources as a Streamlined Pathway to DNA Origami Assembly and Testing

This paper introduces a method to isolate ssDNA from dsDNA sources for DNA origami assembly, demonstrating its effectiveness across various dsDNA types and lengths.

TMC1 and TMC2 are cholesterol-dependent scramblases that regulate membrane homeostasis in auditory hair cells

This study identifies TMC1 and TMC2 as cholesterol-dependent lipid scramblases that regulate membrane homeostasis in auditory hair cells, linking their dysfunction to hereditary deafness.

Groove architecture controls lipid scrambling in simulations of protein and model systems

This study uses simulations to show that groove architecture, not amino acid sequence, determines lipid scrambling in scramblase proteins.

Complexes of vertebrate TMC1/2 and CIB2/3 proteins form hair-cell mechanotransduction cation channels

The paper shows that CIB2/3 and TMC1/2 form complexes essential for hair-cell mechanotransduction in vertebrates, supported by structural and functional analyses.

Transmembrane channel-like 4 and 5 proteins at microvillar tips are potential ion channels and lipid scramblases

The paper identifies TMC4 and TMC5 at microvillar tips and suggests they may function as ion channels and lipid scramblases, similar to mechanotransduction complexes in stereocilia.

In-Silico Analyses of Molecular Force Sensors for Mechanical Characterization of Biological Systems

This paper uses molecular dynamics simulations to analyze how design parameters affect the mechanical properties of three types of molecular force sensors.

Elasticity and Thermal Stability are Key Determinants of Hearing Rescue by Mini-Protocadherin-15 Proteins

The paper identifies elasticity and thermal stability as critical factors determining the effectiveness of mini-protocadherin-15 proteins in rescuing hearing in USH1F mouse models.