Biomolecules
In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin the Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic…
The wobble hypothesis does not discriminate between uracil and thymine. Methylation could favor further stabilization of uracil in the keto form. Thymine is present in keto form only and can pair up but with adenine. Uracil can easily…
To what extent must a hydrophobic gate expand for the channel to count as open? We address this question using the nicotinic acetylcholine receptor (nAChR) as the exemplar. The nAChR is an integral membrane protein which forms a cation…
In this paper, we model the mechanics of a collagen pair in the connective tissue extracellular matrix that exists in abundance throughout animals, including the human body. This connective tissue comprises repeated units of two main…
Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and…
In the template-assistance model, normal prion protein (PrPC), the pathogenic cause of prion diseases such as Creutzfeldt-Jakob (CJD) in human, Bovine Spongiform Encephalopathy (BSE) in cow, and scrapie in sheep, converts to infectious…
We investigate the mechanical unfolding of the tenth type III domain from fibronectin, FnIII10, both at constant force and at constant pulling velocity, by all-atom Monte Carlo simulations. We observe both apparent two-state unfolding and…
The presence of oligomeric aggregates, which is often observed during the process of amyloid formation, has recently attracted much attention since it has been associated with neurodegenerative conditions such as Alzheimer's and Parkinson's…
Peptides and proteins exhibit a common tendency to assemble into highly ordered fibrillar aggregates, whose formation proceeds in a nucleation-dependent manner that is often preceded by the formation of disordered oligomeric assemblies.…
Understanding the molecular determinants of specificity in protein-protein interaction is an outstanding challenge of postgenome biology. The availability of large protein databases generated from sequences of hundreds of bacterial genomes…
Renaturation and hybridization reactions lead to the pairing of complementary single-stranded nucleic acids. We present here a theoretical investigation of the mechanism of these reactions in vitro under thermal conditions (dilute solutions…
The interior of cells is crowded thus making it important to assess the effects of macromolecules on the folding of proteins. Using the Self-Organized Polymer (SOP) model, which is a coarse-grained representation of polypeptide chains, we…
Protein identification is one of the major task of Proteomics researchers. Protein identification could be resumed by searching the best match between an experimental mass spectrum and proteins from a database. Nevertheless this approach…
The accurate prediction and characterization of DNA melting domains by computational tools could facilitate a broad range of biological applications. However, no algorithm for melting domain prediction has been available until now. The main…
The protective effect exerted by polyamines (Put and Spd) against cadmium (Cd) stress was investigated in Brassica juncea plants. Treatment with CdCl2 (75 micro-Mole) resulted in a rise of Cd accumulation, a decrease of fresh and dry…
In 1994, I conjectured that insulin-degrading enzyme (IDE) acts as an inhibitor of malignant transformation by degrading insulin and thus preventing this major growth-stimulatory hormone from binding and thereby inactivating the…
We perform molecular dynamics simulations for a simple coarse-grained model of crambin placed inside of a softly repulsive sphere of radius R. The confinement makes folding at the optimal temperature slower and affects the folding…
We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether ``breather'' solitons could play a role in the…
The equilibrium three dimensional shape of relatively short loops of DNA is studied using an elastic model that takes into account anisotropy in bending rigidities. Using a reasonable estimate for the anisotropy, it is found that cyclized…
The protein backbone is described as a smooth curved and twisted line in three-dimensional (3D) space and characterized by its curvature $\kappa(s)$ and torsion $\tau(s)$ both expressed as a function of arc length s. It is shown that the…