Related papers: Power and limitations of electrophoretic separatio…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
A new technique for the separation of macromolecules is proposed and investigated. A thin mesh with pores comparable to the radius of gyration of a free chain is used to filter chains according to their length. Without a field it has…
We analyze large systems of interacting proteins, using techniques from the non-equilibrium statistical mechanics of disordered many-particle systems. Apart from protein production and removal, the most relevant microscopic processes in the…
The convergent interests of different scientific disciplines, from biochemistry to electronics, toward the investigation of protein electrical properties, has promoted the development of a novel bailiwick, the so called proteotronics. The…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…
Achieving a comprehensive understanding of the behaviour of proteins is greatly facilitated by the knowledge of their structures, thermodynamics and dynamics. All this information can be provided in an effective manner in terms of…
In Proteomics, only the de novo peptide sequencing approach allows a partial amino acid sequence of a peptide to be found from a MS/MS spectrum. In this article a preliminary work is presented to discover a complete protein sequence from…
Mass spectrometry provides a high-throughput approach to identify proteins in biological samples. A key step in the analysis of mass spectrometry data is to identify the peptide sequence that, most probably, gave rise to each observed…
In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
Proteomics will celebrate its 20th year in 2014. In this relatively short period of time, it has invaded most areas of biology and its use will probably continue to spread in the future. These two decades have seen a considerable increase…
Introduction : Mass spectrometry approaches are very attractive to detect protein panels in a sensitive and high speed way. MS can be coupled to many proteomic separation techniques. However, controlling technological variability on these…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…
Proteins congregate into complexes to perform fundamental cellular functions. Phenotypic outcomes, in health and disease, are often mechanistically driven by the remodeling of protein complexes by protein coding mutations or cellular…
Capillary electrophoresis has long been been recognized as a powerful analytic tool. Here it is demonstrated that the same capillary electrophoretic experiments also reveal dynamic properties of the polymer solutions being used as the…
The full understanding of cellular functions requires information about protein numbers for various biomolecular assemblies and their dynamics, which can be partly accessed by super-resolution fluorescence microscopy. Yet, many protein…
The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…