Rotamer decomposition and protein dynamics: Efficiently analyzing dihedral populations from molecular dynamics

Molecular mechanics methods have matured into powerful methods to understand the dynamics and flexibility of macromolecules and especially proteins. As multinanosecond to microsecond length molecular dynamics (MD) simulations become commonplace, advanced analysis tools are required to generate scientifically useful information from large amounts of data. Some of the key degrees of freedom to understand protein flexibility and dynamics are the amino acid residue side chain dihedral angles. In this work, we present an easily automated way to summarize and understand the relevant dihedral populations. A tremendous reduction in complexity is achieved by describing dihedral timeseries in terms of histograms decomposed into Gaussians. Using the familiar and widely studied protein lysozyme, it is demonstrated that our approach captures essential properties of protein structure and dynamics. A simple classification scheme is proposed that indicates the rotational state population for each dihedral angle of interest and allows a decision if a given side chain or peptide backbone fragment remains rigid during the course of an MD simulation, adopts a converged distribution between conformational substates or has not reached convergence yet. © 2012 Wiley Periodicals, Inc.     

Comment on “Extending Hirshfeld‐I to bulk and periodic materials”

In recent years, several methods have been developed that partition the electron density among atoms using spherically symmetric atomic weights. D. E. P. Vanpoucke, P. Bultinck, and I. Van Driessche (J. Comput. Chem. 2012, doi: 10.1002/jcc.23088) recently reported a periodic implementation of the Hirshfeld‐I method that uses a combination of Becke‐style and uniform integration grids and modified atomic reference densities to compute net atomic charges in periodic materials. Herein, this method is discussed in the context of earlier periodic implementations of the Hirshfeld‐I method, the Iterated Stockholder Atoms method, and the density derived electrostatic and chemical method.     

A new mathematical model for the enzymatic kinetic resolution of racemates

A mathematical model is presented for the kinetic resolution of racemates. It takes all intermediate binding steps into account and assumes that such steps are reversible. The model describing dynamics of the chiral reaction products consists of two nonlinear differential equations. With this model, the enantioselectivity of enzyme has been studied. Mathematical and numerical simulation of the model show that there are several ways to control the enantiomeric ratio (E) but the affinity and the binding rates of the intermediate enzyme complex to the racemic substrates are the key steps for the enzyme enantioselectivity.     

The stereochemistry of glycolipids. A key for understanding membrane functions?

A Commentary on the paper ”Studies on liquid‐crystalline glycosides" by Volkmar Vill, Thomas Böcker, Joachim Thiem and Fred Fischer. First published in Liquid Crystals, 6, 349‐356 (1989).     

Effect of the twisted alignment on the liquid crystal wave‐front corrector

The effect of twisted alignment on the phase modulation of a liquid crystal wave‐front corrector was investigated. First, the effect of twisted alignment is discussed in terms of the modulation principle of the liquid crystal molecule. Only partial incident light can be modulated because of the effect of the twisted alignment. Other unmodulated light will affect the correction accuracy and the resolution of the image. The blazed grating method is proposed to solve this problem. Adaptive correction was performed without the blazed grating method and the correction results are poor. A similar adaptive correction experiment was performed with the blazed grating method and a better correction result is obtained. The residual averaged wave‐front errors are PV = 0.101λ and RMS = 0.015λ and a resolvable image is obtained.     

Virtual isotropic‐nematic transitions in alkyl cyanobiphenyls

Pretransitional fluctuations in the isotropic phase of liquid crystalline and non‐liquid crystalline alkyl cyanobiphenyls have been investigated using light scattering and magnetic birefringence measurements. We find evidence for a virtual isotropic‐nematic phase transition in short‐chain alkyl cyanobiphenyls with no observable nematic phase. The measured temperature dependence of fluctuations is well‐described by mean‐field theory. Virtual phase transition temperatures extrapolated from separate light scattering and magnetic birefringence experiments are in good agreement. Landau–de Gennes model parameters for the compounds investigated are calculated from the experimental results.     

MS Analysis and Molecular Characterization of Botrytis cinerea Protease Prot-2. Use in Bioactive Peptides Production

Prot-2 protease previously purified to homogeneity from Botrytis cinerea showed potentiality to be used in detergency and for production of bioactive peptides. To extend the characterization of Prot-2 protease, antifungal and antibacterial assays were performed in vitro using protein hydrolysates prepared from muscle of mackerel (Scomber scomborus) treated with this enzyme. The most active hydrolysate (degree of hydrolysis of 8 %) exhibited inhibition effect towards bacteria and phytopathogenic fungi, demonstrating that Prot-2 proteolysis generated bioactive peptides. Biochemical and molecular characterization of the purified Prot-2, by SDS-PAGE/Tryptic in gel-digestion and LC-MS/MS analysis, was investigated. The peptide amino acid sequence alignment search in database revealed a moderate homology between the determined amino acid sequence of Prot-2 protease and the known fungal trypsin/chymotrypsin in particular from Glomerella, Metarhizium and Streptomyces. From peptide sequence data obtained by mass spectrometry and sequences homologies, primers were defined and a cDNA fragment of 786 bp was amplified by RT-PCR. The cDNA nucleotide sequence analysis revealed an open reading frame coding for 262 amino acid residues. The deduced amino acid sequence of Prot-2 showed moderate identity with trypsin of Glomerella graminicola (74 %) and with chymotrypsin from Metarhizium anisopliae (71 %). Prot-2 exhibited a Ser protease homology and showed in addition the specific His motif of trypsin/chymotrypsin family.     

Prearranged Glycosides,Part 10. Intramolecular Glycosylation with Cellobiosyl,Lactosyl, and Maltosyl Donors

ABSTRACT

Acetyl protected 1,2-O-(1-methoxyethylidene)-disaccharides 1 of maltose, cellobiose, and lactose, respectively were converted via the corresponding benzyl protected couterparts 2, the benzyl protected phenyl 2-O-acetyl- 3 and 2-O-unprotected 1-thio-glycoside disaccharides 4 into 2-O-succinoylated disaccharides 5. The latter were esterified with benzyl 2-O-benzoyl-4,6-di-O-benzylidene-α-D-glucopyranoside (6) to afford succinyl linked derivatives 7 the benzylidene groups of which were regioselectively opened to give prearranged glycoside trisaccharides 8. Intramolecular glycosylation of the latter with N-iodosuccinimide resulted in exclusive formation of the corresponding α-(1→4)-linked trisaccharides 9. No influence of the donor moiety on the diastereoselectivity of the intramolecular glycosylation was observed.