PUBLICATIONS
2024
Biophysical studies of the promiscuous transcription factor engrailed: Proposed mechanism for the conformational response by electrostatics and DNA recognition
B Tanielian, M Sadqi, V Munoz
Biophysical Journal 123 (3), 198a
Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins
C Ghosh, S Nagpal, V Muñoz
Current Opinion in Structural Biology 84, 102756
2023
Engineering of a Broadband Genetically Encodable Ratiometric Fluorescent Calcium Biosensor with a 1 ms Folding Time in Response to Calcium
J Rodriguez-Reyes, D Gravano, M Sadqi, V Munoz
PROTEIN SCIENCE 32 (12)
Towards an Accurate Prediction of Protein (Un) Folding Rates and Stability from Structure and Sequence
M Abdulqader, V Munoz
PROTEIN SCIENCE 32 (12)
A Dimer-Partner Tug of War Mechanism for Building Fluorescence Protein Biosensors for the Detection of SARS-CoV-2
K Ramirez, D Bouzada, A Bains, M Sadqi, P Liwang, E Sentis-Vazquez, …
PROTEIN SCIENCE 32 (12)
Compliant mechanical response of the ultrafast folding protein EnHD under force
A Reifs, I Ruiz Ortiz, AO Saa, J Schönfelder, D De Sancho, V Muñoz, …
Communications Physics 6 (1), 7
How to Scan DNA using Promiscuous Recognition and No Sliding Clamp: A Model for Pioneer Transcription Factors
RR Goluguri, M Sadqi, S Nagpal, V Muñoz
bioRxiv, 2023.05. 16.541005
Track: Synthetic Biology & Biosensing: Engineering Protein Components A Dimer-Partner Tug of War Mechanism for Building Fluorescence Protein Biosensors for the Detection of …
K Ramirez, D Bouzada, M Sadqi, E Vazquez, V Munoz
PROTEIN SCIENCE 32
Synthetic Biology & Biosensing: Engineering Protein Components Engineering of genetically encoded ratiometric fluorescent calcium biosensors with broadband sensitivity and 1 ms …
J Rodriguez-Reyes, A Sengupta, M Sadqi, V Munoz
PROTEIN SCIENCE 32
Track: Protein and Ligand-A New Marriage Between an Old Couple Resolving the kinetics of transcription factor recognition of the target DNA site via advanced single-molecule …
C Ghosh, M Sadqi, V Munoz
PROTEIN SCIENCE 32
2022
A modular approach to map out the conformational landscapes of unbound intrinsically disordered proteins
TDN Luong, S Nagpal, M Sadqi, V Muñoz
Proceedings of the National Academy of Sciences 119 (23), e2113572119
First Year of Biophysica
Buck, V Muñoz
Biophysica 2 (2), 89-90
Cognate DNA Recognition by Engrailed Homeodomain Involves A Conformational Change Controlled via An Electrostatic-Spring-Loaded Latch
N D’Amelio, B Tanielian, M Sadqi, P López-Navajas, V Muñoz
International Journal of Molecular Sciences 23 (5), 2412
Engrailed homeodomain uses an electrostatic spring-loaded mechanism to change conformation upon binding to DNA
B Tanielian, N d’Amelio, M Sadqi, V Munoz
Biophysical Journal 121 (3), 18a-19a
Transcriptional factors control their diffusion on DNA by modulating their dynamics
RR Goluguri, M Sadqi, V Munoz
Biophysical Journal 121 (3), 457a
Protein Folding: Methods and Protocols
V Muñoz
HumanaPress
Prediction of Folding and Unfolding Rates of Proteins with Simple Models
D De Sancho, V Muñoz
Protein Folding: Methods and Protocols, 365-372
Single-Molecule Fluorescence Spectroscopy Approaches for Probing Fast Biomolecular Dynamics and Interactions
Z Wang, N Mothi, V Muñoz
Protein Folding: Methods and Protocols, 235-246
NMR Relaxation Dispersion Methods for the Structural and Dynamic Analysis of Quickly Interconverting, Low-Populated Conformational Substates
S Veeramuthu Natarajan, N D’amelio, V Muñoz
Protein Folding: Methods and Protocols, 187-203
Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms
X Chu, S Nagpal, V Muñoz
Protein Folding: Methods and Protocols, 343-362
2021
Protein folding dynamics as diffusion on a free energy surface: rate equation terms, transition paths, and analysis of single-molecule photon trajectories
N Mothi, V Muñoz
The Journal of Physical Chemistry B 125 (45), 12413-12425
Functional Role of Protein Disorder in Eukaryotic Gene Regulation
RR Goluguri, M Sadqi, S Nagpal, V Munoz
PROTEIN SCIENCE 30, 64-64
Biophysica—A New International Open Access Journal to Integrate Across the Modern Biophysical Sciences and Engineering
M Buck, V Muñoz
Biophysica 1 (1), 73-75
2020
Lessons about Protein Folding and Binding from Archetypal Folds, Luis Alberto Campos, Mourad Sadqi & Victor Muñoz (2020) Accounts of Chemical Research.
Downhill (Un) Folding Coupled to Binding as Mechanism for Engineering Broadband Protein Conformational Transducers, Suhani Nagpal, Thinh D.N. Luong, Mourad Sadqi & Victor Muñoz (2020) ACS Synthetic Biology 9,9.
Eukaryotic transcription factors can track and control their target genes using DNA antennas, Milagros Castellanos, Nivin Mothi & Victor Muñoz (2020) Nature Communications 11, 540.
2019
Engineering protein assemblies with allosteric control via monomer fold-switching., Luis A. Campos, Rajendra Sharma, Sara Alvira, Federico M. Ruiz, Beatriz Ibarra-Molero, Mourad Sadqi, Carlos Alfonso, Germán Rivas, Jose M. Sanchez-Ruiz, Antonio Romero Garrido, José M. Valpuesta & Victor Muñoz (2019) Nature Communications 10, 5703.
Ultrafast folding kinetics of WW domains reveal how the amino acid sequence determines the speed limit to protein folding , Malwina Szczepaniak, Manuel Iglesias-Bexiga, Michele Cerminara, Mourad Sadqi, Celia Sanchez de Medina, Jose C Martinez, Irene Luque, Victor Muñoz (2019) Proceedings of the National Academy of Sciences 116 (17) 8137-8142.
Glutton: a tool for generating structural ensembles of partly disordered proteins from chemical shifts , Yi He, Suhani Nagpal, Mourad Sadqi, Eva de Alba, Victor Muñoz (2019) Bioinformatics, 35, 7, 1234–1236.
2018
Reversible two-state folding of the ultrafast protein gpW under mechanical force, Jörg Schönfelder, David De Sancho, Ronen Berkovich, Robert B. Best, Victor Muñoz & Raul Perez-Jimenez (2018) Communications Chemistry 1, 59.
Instrumental effects in the dynamics of an ultrafast folding protein under mechanical force , David De Sancho, Jörg Schönfelder, Robert B. Best, Raul Perez-Jimenez, and Victor Muñoz (2018) The Journal of Physical Chemistry B 122, 49, 11147–11154.
Protein Folding Cooperativity and Thermodynamic Barriers of the Simplest β-Sheet Fold: A Survey of WW Domains , Manuel Iglesias-Bexiga, Malwina Szczepaniak, Celia Sanchez de Medina, Eva S. Cobos, Raquel Godoy-Ruiz,§ Jose C. Martinez, Victor Muñoz*, and Irene Luque* (2018) The Journal of Physical Chemistry B 122, 49, 11058–11071.
2017
Interplay between the folding mechanism and binding modes in folding coupled to binding processes, R. Sharma, D. De Sancho & V. Muñoz (2017) Physical Chemistry Chemical Physics 19, 28512-28516.
Interplay between downhill folding and conformational disorder modulates DNA recognition of DNA binding domains , X. Chu and V. Muñoz (2017) Physical Chemistry Chemical Physics 19(42):28527-28539.
2016
Chapter 12 — Modern Analysis of Protein Folding by Differential Scanning Calorimetry, B Ibarra-Molero, AN Naganathan, JM Sanchez-Ruiz, V Muñoz. (2016) Methods in Enzymology 567, 281-318.
When Fast is Better: Protein Folding Fundamentals and Mechanisms from Ultrafast Approaches, V Muñoz, M Cerminara (2016) Biochemical Journal 473 (17), 2545-2559.
A Simple Two-state Protein Unfolds Mechanically via Multiple Heterogeneous Pathways at Single-molecule Resolution, J Schönfelder, R Perez-Jimenez, V Muñoz (2016) Nature Communications 7:11777.
Limited Cooperativity in Protein Folding, V Muñoz, LA Campos, M Sadqi (2016) Current Opinion in Structural Biology 36, 58-66.
2015
A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories, R Ramanathan, V Muñoz (2015) The Journal of Physical Chemistry B 119 (25), 7944-7956.
Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations, L Sborgi, A Verma, S Piana, K Lindorff-Larsen, M Cerminara, C M Santiveri, D Shaw, E de Alba, V Muñoz (2015) Journal of the American Chemical Society 137 (20), 6506-6516.
2014
A Simple Theoretical Model Goes a Long Way in Explaining Complex Behavior in Protein Folding, V Muñoz (2014) Proceedings of the National Academy of Sciences 111 (45), 15863-15864.
Thermodynamics of Downhill Folding: Multi-Probe Analysis of PDD, a Protein that Folds Over a Marginal Free Energy Barrier, AN Naganathan, V Muñoz (2014) The Journal of Physical Chemistry B 118 (30), 8982-8994
Impact of Atomistic Molecular Dynamics Simulations on Understanding how Proteins Fold: An Experimentalist’s Perspective. WA Eaton, V Muñoz (2014) Bioinformatics 22.
Probing the Free Energy Landscape of the Fast-Folding gpW Protein by Relaxation Dispersion NMRs, C Sanchez-Medina, A Sekhar, P Vallurupalli, M Cerminara, V Muñoz, …(2014) Journal of the American Chemical Society 136 (20), 7444-7451.
2013
Slow Proton Transfer Coupled to Unfolding Explains the Puzzling Results of Single-molecule Experiments on BBL, a Paradigmatic Downhill Folding Protein, M Cerminara, LA Campos, R Ramanathan, V Muñoz, LE Key (2013) PloS One 8 (10), e78044.
Gradual Disordering of the Native State on a Slow Two-State Folding Protein Monitored by Single-Molecule Fluorescence Spectroscopy and NMR, LA Campos, M Sadqi, J Liu, X Wang, DS English, V Muñoz (2013) The Journal of Physical Chemistry B 117 (42), 13120-13131.
Reply to Huang et al.: Slow Proton Exchange can Duplicate the Number of Species Observed in Single-molecule Experiments of Protein Folding, LA Campos, V Muñoz (2013) Proceedings of the National Academy of Sciences 110 (14), E1242-E1243.
Protein Folding at Atomic Resolution: Analysis of Autonomously Folding Supersecondary Structure Motifs by Nuclear Magnetic Resonance, L Sborgi, A Verma, M Sadqi, E de Alba, V Muñoz (2013) Protein Supersecondary Structures, 205-218.