Serine proteases are the most versatile proteolytic enzymes with tremendous applications in various industrial processes. This study was designed to investigate biochemical properties, critical residues, and catalytic potential of alkaline serine protease using in-silico approaches. The primary sequence analyzed ProtParam, SignalP, Phyre2 tools signal peptide, secondary structure, respectively....

Lipid formulations can improve the bioavailability of drugs that have low aqueous solubility. A variety of chemical compounds, including triglyceride oils (lipids), fatty acid esters and surfactants, can be included in lipid formulations. This heterogeneity makes spectroscopic study of the in ternal structure of formulation difficult. Understanding of lipid formulations at a molecular level wil...

~:onvCrsiOn Of fOreSr hd LO ~grklJhrid IJSCS occurred rhrougboul Ltlc region over the past 200 years. IJresendy. Forc\rv cnvcr less rhnn one-quarrcr of Abe area of +&srI:md prior to European se&mrnr. Most recmrly, widcscalc loss of foresr cnver occurd during rhc early in response ro increnscs in soybean priceb (Srrrnirlk.kc: 1976). ln many casts, these 1asL Iim3rs ro IJ~ clrnrcd occupied sites ...

The study of membranes and embedded proteins represents an advanced task in the field of molecular simulation. While nowadays a profound selection of sampling techniques, molecular topologies and theoretical approaches is available, the analysis of actual simulation data remains a difficult endeavour. For homogeneous lipid bilayer simulations, the calculation of the bilayer thickness or area pe...

The MoSGrid (Molecular Simulation Grid) project is currently establishing a platform that aims to be used by both experienced and inexperienced researchers to submit molecular simulation calculations, monitor their progress, and retrieve the results. It provides a web-based portal to easily set up, run, and evaluate molecular simulations carried out on D-Grid resources. The range of application...

A limitation of traditional molecular dynamics (MD) is that reaction rates are difficult to compute. This is due to the rarity of observing transitions between metastable states since high energy barriers trap the system in these states. Recently the weighted ensemble (WE) family of methods have emerged which can flexibly and efficiently sample conformational space without being trapped and all...

Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the ato...

Protein-protein interactions encode the wiring diagram of cellular signaling pathways and their deregulations underlie a variety of diseases, such as cancer. Inhibiting protein-protein interactions with peptide derivatives is a promising way to develop new biological and therapeutic tools. Here, we develop a general framework to computationally handle hundreds of non-natural amino acid sidechai...

Type1 restriction modification system are intriguing multifunctional multisubunit molecular motors that can catalyze both restriction and modification activity. The type 1 RM enzymes binds to its target sequence and its activity as an endonuclease or methyltransferase is determined by the methylation state of the target sequence. If the target sequence is unmodified, the enzyme while bound to i...

Surfactant proteins are of major importance for the stability and flexibility of lipid systems like the lung surfactant or the tear film. They can support the adsorption of phospholipids into a layer or specifically influence the surface tension of a lipid surface [1]. To fulfil these functions, they are described to be highly posttranslationally modified. Furthermore, immunological functions w...