Bioquímica i Biomedicina Molecular: Recent submissions
Now showing items 681-700 of 919
Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance
Relaxases are metal-dependent nucleases that break and join DNA for the initiation and completion of conjugative bacterial gene transfer. Conjugation is the main process through which antibiotic resistance spreads among ...
Multiscale simulation of DNA
DNA is not only among the most important molecules in life, but a meeting point for biology, physics and chemistry, being studied by numerous techniques. Theoretical methods can help in gaining a detailed understanding of ...
Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes
Modification of SMN2 exon 7 (E7) splicing is a validated therapeutic strategy against spinal muscular atrophy (SMA). However, a target-based approach to identify small-molecule E7 splicing modifiers has not been attempted, ...
4D Genome rewiring during oncogene-induced and replicative senescende
To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome, replication-timing, whole-genome bisulfite sequencing, and gene ...
The differential response of proteins to macromolecular crowding
The habitat in which proteins exert their function contains up to 400 g/L of macromolecules, most of which are proteins. The repercussions of this dense environment on protein behavior are often overlooked or addressed ...
Challenges and guidelines toward 4D nucleome data and model standards
Due to recent advances in experimental and theoretical approaches, the dynamic three-dimensional organization (3D) of the nucleus has become a very active area of research in life sciences. We now understand that the linear ...
Prediction and validation of protein intermediate states from structurally rich ensembles and coarse grained simulations
Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making ...
Residues coevolution guides the systematic identification of alternative functional conformations in proteins
We present here a new approach for the systematic identification of functionally relevant conformations in proteins. Our fully automated pipeline, based on discrete molecular dynamics enriched with coevolutionary information, ...
Reduced alfa-MSH underlies hypothalamic ER-stress-induced hepatic gluconeogenesis
Alterations in ER homeostasis have been implicated in the pathophysiology of obesity and type-2 diabetes (T2D). Acute ER stress induction in the hypothalamus produces glucose metabolism perturbations. However, the ...
Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor.
Newly discovered bacterial photoreceptors called CarH sense light by using 5′-deoxyadenosylcobalamin (AdoCbl). They repress their own expression and that of genes for carotenoid synthesis by binding in the dark to operator ...
Understanding the Connetion between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations
Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression. Here, we have examined the effect of epigenetic DNA methylation on nucleosomal stability using molecular ...
Molecular dynamics study of natural existing cavity couplings in proteins
Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regu- lation. In this article we have studied the ...
Difining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case
The early stages of the thermal unfolding of apoflavodoxin have been determined by using atomistic multi microsecond-scale molecular dynamics (MD) simulations complemented with a variety of experimental techniques. Results ...
CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes
We present CGeNArate, a new model for molecular dynamics simulations of very long segments of B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained Hamiltonian with ...
Long-timescale dynamics of the Drew-Dickerson dodecamer
We present a systematic study of the long-timescale dynamics of the Drew-Dickerson dodecamer (DDD: d(CGCGAATTGCGC)2) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the ...
DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p.
The mitochondrial genome (mtDNA) is assembled into nucleo-protein structures termed nucleoids and maintained differently compared to nuclear DNA, the involved molecular basis remaining poorly understood. In yeast (Saccharomyces ...
Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins
We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation ...
A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids
The physicochemical properties of nucleic acids are dominated by their highly charged phosphodiester backbone chemistry. The polyelectrolyte structure decouples information content (base sequence) from bulk properties ...
An In-Depth Look at DNA Crystals through the Prism of Molecular Dynamics Simulations
X-ray crystallography is the primary tool for biomolecular structural determination. However, contacts formed through the crystal lattice are known to affect structures, especially for small and flexible molecules such as ...
The (In)dependence of Alternative Splicing and Gene Duplication.
Alternative splicing (AS) and gene duplication (GD) both are processes that diversify the protein repertoire. Recent examples have shown that sequence changes introduced by AS may be comparable to those introduced by GD. ...
