Related papers: The Role of Structure in the Protein Dynamical Tra…
Emergence of new protein structures has proved difficult to trace in nature and engineer in the laboratory. However, one aspect of structure evolution has proved immensely helpful for determining the three-dimensional structure of proteins…
An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good…
Azido-modified alanine residues (AlaN$_3$) are environment-sensitive, minimally invasive infrared probes for the site-specific investigation of protein structure and dynamics. Here, the capability of the label is investigated to query…
A simple and predictive model is put forward explaining the experimentally observed substantial shift of the glass transition temperature, Tg, of sufficiently thin polymer films. It focuses on the limit of small molecular weight, where…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
We present results of a hole burning study with thermal cycling and waiting time spectral diffusion experiments on a modified cytochrome - c protein in its native as well as in its denatured state. The experiments show features which seem…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
Electron paramagnetic resonance signal parameters of TEMPO dichlorotriazine and TEMPO maleimide spin labels attached to protein human serum albumin molecules have been monitored at various temperatures, salts and sucrose concentrations. The…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…
Terahertz time domain spectroscopy (THz TDS) is used to measure the melting kinetics of fructose molecular crystals. Combining single crystal anisotropy measurements with density functional calculations we assign the phonon frequencies and…
The respective roles of local and nonlocal interactions in the thermodynamic cooperativity of proteins are investigated using continuum (off-lattice) native-centric G\=o-like models with a coarse-grained C$_\alpha$ chain representation. We…
The proposal of this paper is to provide a simple angular random walk model to build up polypeptide structures, which encompass properties of dihedral angles of folded proteins. From this model, structures will be built with lengths ranging…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
Liquid water is one of the most studied substances, yet many of its properties are difficult to rationalize. The uniqueness of water is rooted in the dynamic network of hydrogen-bonded molecules with relaxation time constants of about one…
Structural balance in social complex networks has been modeled with two types of triplet interactions. First, the interaction that only considers dynamic role for links or relationships (Heider balance), and second, the interaction that…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Although the importance of protein dynamics in protein function is generally recognized, the role of protein fluctuations in allosteric effects scarcely has been considered. To address this gap, the Kullback-Leibler divergence (Dx) between…
A quantum mechanical model on histone modification is proposed. Along with the methyl / acetate or other groups bound to the modified residues the torsion angles of the nearby histone chain are supposed to participate in the quantum…