Quasiclassical trajectory calculations of collisional energy transfer in propane systems: multiple direct-encounter hard-sphere model

Quasiclassical trajectory calculations of collisional energy transfer from highly vibrationally excited propane + rare gas systems are reported. This work extends our hard-sphere model (A. Linhananta and K. F. Lim, Phys. Chem. Chem. Phys., 2000, 2, 1385) to examine the variation of the internal energy during collisions with a rare bath gas. This was accomplished by recording the vibrational and rotational energy of propane after each atom&ndash;atom encounter during trajectory simulations of propane + rare gas systems. This provides detailed information of the energy flow during a collision. It was found that collisions with small number of encounters transfer energy efficiently, whereas those with many encounters do not. Detailed analyses reveal that the former collisions arise from trajectories with high initial impact parameter, whereas the latter have small initial impact parameter. The reason behind this is the dependence of collision energy transfer (CET) of large polyatomic molecules on their shape. This is connected to the well-known role of rotational energy transfer (RET) as a gateway for CET.<br /

Toy amphiphiles on the computer: What can we learn from generic models?

Generic coarse-grained models are designed such that they are (i) simple and (ii) computationally efficient. They do not aim at representing particular materials, but classes of materials, hence they can offer insight into universal properties of these classes. Here we review generic models for amphiphilic molecules and discuss applications in studies of self-assembling nanostructures and the local structure of bilayer membranes, i.e. their phases and their interactions with nanosized inclusions. Special attention is given to the comparison of simulations with elastic continuum models, which are, in some sense, generic models on a higher coarse-graining level. In many cases, it is possible to bridge quantitatively between generic particle models and continuum models, hence multiscale modeling works on principle. On the other side, generic simulations can help to interpret experiments by providing information that is not accessible otherwise.Comment: Invited feature article, to appear in Macromolecular Rapid Communication

Modeling Elasticity in Crystal Growth

A new model of crystal growth is presented that describes the phenomena on atomic length and diffusive time scales. The former incorporates elastic and plastic deformation in a natural manner, and the latter enables access to times scales much larger than conventional atomic methods. The model is shown to be consistent with the predictions of Read and Shockley for grain boundary energy, and Matthews and Blakeslee for misfit dislocations in epitaxial growth.Comment: 4 pages, 10 figure

Genetically encoded photocross-linkers determine the biological binding site of exendin-4 peptide in the N-terminal domain of the intact human glucagon-like peptide-1 receptor (GLP-1R)

The glucagon-like peptide-1 receptor (GLP-1R) is a key therapeutic target in the management of type II diabetes mellitus, with actions including regulation of insulin biosynthesis and secretion, promotion of satiety, and preservation of β-cell mass. Like most class B G protein-coupled receptors (GPCRs), there is limited knowledge linking biological activity of the GLP-1R with the molecular structure of an intact, full-length, and functional receptor·ligand complex. In this study, we have utilized genetic code expansion to site-specifically incorporate the photoactive amino acid p-azido-l-phenylalanine (azF) into N-terminal residues of a full-length functional human GLP-1R in mammalian cells. UV-mediated photolysis of azF was then carried out to induce targeted photocross-linking to determine the proximity of the azido group in the mutant receptor with the peptide exendin-4. Cross-linking data were compared directly with the crystal structure of the isolated N-terminal extracellular domain of the GLP-1R in complex with exendin(9–39), revealing both similarities as well as distinct differences in the mode of interaction. Generation of a molecular model to accommodate the photocross-linking constraints highlights the potential influence of environmental conditions on the conformation of the receptor·peptide complex, including folding dynamics of the peptide and formation of dimeric and higher order oligomeric receptor multimers. These data demonstrate that crystal structures of isolated receptor regions may not give a complete reflection of peptide/receptor interactions and should be combined with additional experimental constraints to reveal peptide/receptor interactions occurring in the dynamic, native, and full-length receptor state

Structural and functional stabilization of protein entities: state-of-the-art

Within the context of biomedicine and pharmaceutical sciences, the issue of (therapeutic) protein stabilization assumes particular relevance. Stabilization of protein and protein-like molecules translates into preservation of both structure and functionality during storage and/or targeting, and such stabilization is mostly attained through establishment of a thermodynamic equilibrium with the (micro)environment. The basic thermodynamic principles that govern protein structural transitions and the interactions of the protein molecule with its (micro)environment are, therefore, tackled in a systematic fashion. Highlights are given to the major classes of (bio)therapeutic molecules, viz. enzymes, recombinant proteins, (macro)peptides, (monoclonal) antibodies and bacteriophages. Modification of the microenvironment of the biomolecule via multipoint covalent attachment onto a solid surface followed by hydrophilic polymer co-immobilization, or physical containment within nanocarriers, are some of the (latest) strategies discussed aiming at full structural and functional stabilization of said biomolecules.Financial support to Victor M. Balcao, via an Invited Research Scientist fellowship (FAPESP Ref. No. 2011/51077-8), and project funding (FAPESP Ref. No. 2013/03181-6, Project PneumoPhageKill) by Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP, Sao Paulo, Brazil), is hereby gratefully acknowledged. The authors are also grateful to Claudio M. Barroso (BSc.), Graphic Designer at University of Sorocaba (UNISO), for computer-designing the schemes/drawings integrating this review paper

Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions

Multiple-Well, multiple-path unimolecular reaction systems. II. 2-methylhexyl free radicals

Vibrationally excited 2-methylhexyl radicals formed by shock wave activation or by chemical activation can isomerize by multiple pathways to form any of six stable isomers, can fragment by multiple C[bond]H and C[bond]C bond fission pathways, and can be collisionally stabilized. Master equation simulations of chemical activation and of shock wave activation are used to explore the generic behavior of this complicated coupled system. Selecting the argon pressure in chemical activation systems that produce the 2-methyl-1-hexyl radical isomer ( 1 ) can control the yield of specific isomers. Shock heating of 1 also shows a highly regular sequence of isomer formation. This regular behavior is because the first isomerization steps are faster than subsequent steps. Other radical isomers, such as 2-methyl-3-hexyl ( 3 ), do not show such regular behavior, because the first isomerization step is slower than subsequent steps. Incubation and unimolecular rate-constant fall-off are observed in the shock wave simulations. The unimolecular rate-constant fall-off for the coupled system produces low-pressure limiting rate constants proportional to [M] n , where n can be greater than unity. The fact that n can be greater than unity is a natural feature of multichannel coupled unimolecular reaction systems, but detection of the effect in experiments may be very demanding. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 246–261, 2001Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34897/1/30_ftp.pd