Mechanics of Biomolecules

From atomic workings of nucleic-acids up to protein’s nanomechanical maps.

Biomolecular mechanics play a pivotal role in a myriad of biological processes, influencing everything from the replication and repair of genetic material to the interaction between various biomolecules inside the cell. By deciphering these mechanical properties, we aim to shed light on the inner workings of biological systems, offering physical insights essential for unlocking the mysteries of life itself.

A prime example of our focus lies in the study of double-stranded nucleic acids (DNA and RNA), where mechanical properties dictate crucial biological functions. From the localized movements of individual base pairs upon protein binding to the global folding of genome-length polymers, these biomolecules exhibit a broad spectrum of deformations across multiple length scales. Despite intensive research efforts, bridging the dynamics across these scales remains a formidable challenge.

In our pursuit, we’ve developed a simulation strategies that unveils the atomic underpinnings of nucleic acid mechanics, resolving long-standing paradoxes and offering profound insights. By synergistically combining simulation with experimental techniques such as Atomic Force Microscopy (AFM), Optical Tweezers (OT), and Magnetic Tweezers (MT), we connect our findings to processes occurring on larger scales. Some milestone achievements include:

Solving the paradox of DNA/RNA mechanics:

Resolving a decade-long paradox regarding the differential mechanical response of dsDNA and dsRNA. We’ve uncovered a physical mechanism explaining their counterintuitive twist-stretch behaviors, tracing back to their fundamental differences at the atomic level.

The hidden physical code of the DNA sequence:

Demonstrating that DNA sequence acts not only as a chemical code but also as a physical one. By altering the sequence, we can significantly alter the molecule’s stiffness and correlate these changes with the activation or deactivation of various biological processes. Furthermore, we’ve elucidated how common mutations can reverse these behaviors, finely tuning the DNA’s mechanical and biological responses.

How stiff is a single protein (AFM elasticity maps):

Conducting the first nano-mechanical mapping of a full-sized protein through atomically detailed simulations. This endeavor has not only elucidated the atomic deformations associated with previous Young modulus measurements but has also determined the technique’s spatial resolution limits. Additionally, we’ve uncovered exceptionally high lateral resolution in the non-contact regime, opening new avenues for exploration.

A Marin-Gonzalez, J. G. Vilhena, R Perez, F Moreno-Herrero
A molecular view of DNA flexibility
Quarterly Reviews of Biophysics 54, e8 (2021).

Alberto Marin-Gonzalez, Clara Aicart-Ramos, Mikel Marin-Baquero, Alejandro Martín-González, Maarit Suomalainen, Abhilash Kannan, J G Vilhena, Urs F Greber, Fernando Moreno-Herrero, Rubén Pérez.
Double-stranded RNA bending by AU-tract sequences
Nucleic Acids Research 48 (22), 12917 (2020).

Alberto Marin-Gonzalez,Cesar Pastrana, Rebeca Bocanegra, A. Martín-González, J.G. Vilhena, Ruben Perez, Borja Ibarra, Clara Aicart-Ramos, Fernando Moreno-Herrero.
Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes
Nucleic Acids Research 48 (9), 5024 (2020).

Alberto Marin-Gonzalez, J. G. Vilhena, Fernando Moreno-Herrero, Ruben Perez.
Sequence-dependent mechanical properties of double-stranded RNA
Nanoscale 11, 21471 (2019).

A. Marin-Gonzalez#, J.G. Vilhena#, Fernando Moreno-Herrero, R. Perez.
DNA crookedness regulates DNA mechanical properties at short length scales
Physical Review Letters 122 (4), 048102 (2019). – featured in Nature Reviews Physics

A. Marin-Gonzalez#, J. G. Vilhena#, Ruben Perez, Fernando Moreno-Herrero.
Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom MD
Proceedings of the National Academy of Sciences USA 114 (27), 7049 (2017).