Conformational Properties Of Macromolecules Research Articles

A coarse-grained mechanical model for folding and unfolding of tropoelastin with possible mutations

We propose a simple general framework to predict folding, native states, energy barriers, protein unfolding, as well as mutation induced diseases and other protein structural analyses. The model should not be considered as an alternative to classical approaches (Molecular Dynamics or Monte Carlo) because it neglects low scale details and rather focuses on global features of proteins and structural information. We aim at the description of phenomena that are out of the range of classical molecular modeling approaches due to the large computational cost: multimolecular interactions, cyclic behavior under variable external interactions, and similar. To demonstrate the effectiveness of the approach in a real case, we focus on the folding and unfolding behavior of tropoelastin and its mutations. Specifically, we derive a discrete mechanical model whose structure is deduced based on a coarse graining approach that allows us to group the amino acids sequence in a smaller number of `equivalent’ masses. Nearest neighbor energy terms are then introduced to reproduce the interaction of such amino acid groups. Nearest and non-nearest neighbor energy terms, inter and intra functional blocks are phenomenologically added in the form of Morse potentials. As we show, the resulting system reproduces important properties of the folding-unfolding mechanical response, including the monotonic and cyclic force-elongation behavior, representing a physiologically important information for elastin. The comparison with the experimental behavior of mutated tropoelastin confirms the predictivity of the model. Statement of significanceClassical approaches to the study of phenomena at the molecular scale such as Molecular Dynamics (MD) represent an incredible tool to unveil mechanical and conformational properties of macromolecules, in particular for biological and medical applications. On the other hand, due to the computational cost, the time and spatial scales are limited. Focusing of the real case of tropoelastin, we propose a new approach based on a careful coarse graining of the system, able to describe the overall properties of the macromolecule and amenable of extension to larger scale effects (protein bundles, protein-protein interactions, cyclic loading). The comparison with tropoelastin behavior, also for mutations, is very promising.

Copolymers of 2-Deoxy-2-Methacrylamido-D-Glucose with Aminoacrylates and Allylamine Hydrochloride

New polyvinylsaccharides containing primary or tertiary amino groups were synthesized by radical copolymerization of 2-deoxy-2-methacrylamido-D-glucose (MAG) with 2-(dimethylamino)ethyl methacrylate, 2-(diethylamino)ethyl methacrylate (DEAEM), or allylamine hydrochloride. The reactivity ratios of comonomers were determined. The effect of copolymer composition on the conformational properties of macromolecules was detected. For MAG-DEAEM copolymers with DEAEM unit content more than 60 mol-% the increase of degree of ionization causes conformational transition at α = 0.3 to 0.7 from compact polymer coil to loose coil due to the electrostatic repulsion of charged amino groups. The increase of MAG content in copolymers is accompanied by a decrease of their cytotoxicity.

Hydrodynamic and molecular characteristics of graft copolymers of chitosan with acrylamide

The conformational properties of macromolecules of chitosan and its copolymers with acrylamide in a mixed solvent 0.33 M CH3COOH + 0.3 M NaCl have been investigated by means of translation diffusion and viscometry. The copolymer macromolecules in a solvent suppressing polyelectrolyte effects possess a higher intracoil density (ρav = 0.010 g/cm3) than the chitosan macromolecules (ρav = 0.006 g/cm3), even though the hydrodynamic radius Rh of chitosan is smaller by a factor of ∼1.5.

Conformational properties of macromolecules of heterocyclic polyester imides in dilute dichloroacetic acid solutions

Several series of polyester imides (PEIs) were prepared by melt polycondensation of trimellitimidobenzoic acid and acetylated, substituted hydroquinones as well as by solution polycondensation of corresponding dichlorides with hydroquinones. The influence of either phenyl- or tert-butyl substituents at the hydroquinone unit on the hydrodynamic (diffusion and viscometry) and optical [flow (FB) and electrical (EB) birefringence] properties of solutions of these PEIs were investigated. Independent methods for quantitative evaluation of the length of the statistical Kuhn segment A gave values of 14.5 nm (translational friction and electrical birefringence) and 12.0 nm (flow birefringence), respectively. The equilibrium rigidity of PEIs with phenyl and tert-butyl lateral substituents at the para-aromatic chain fragment was comparable. Conformational properties of the PEIs were analyzed, and the conjugation energies of the ester and amide groups for para-aromatic polyesters, PEIs, and structurally similar polyamidobenzoxazoles and polyamidobenzimidazoles were compared. The introduction of the phthalimide ring leads to a decrease of conjugation energy and deviation of the ester group from coplanarity. The Kuhn segment values obtained were useful for calculations of phase diagrams of semiflexible segmented block copolymers. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 12–24, 2004

Conformational Properties of Macromolecules

<i>Conformational Properties of Macromolecules</i>

Conformational properties of isolated macromolecules

AbstractThe properties of many kinds of solid material (e.g., ionic crystals, quartz, etc.) appear to have only a tenuous correlation with those of the isolated individual atoms or molecules of which they are made. In macromolecular substances, however, thanks primarily to the great strength of covalent bonds, such correlations are strong and indeed essential to fundamental understanding of structure‐property relationships. With certain exceptions, such as polypeptides and polynucleotides with their remarkable helix‐coil transformations, the conformational properties of macromolecules in liquid or amorphous environment are only secondarily dependent on the nature or concentration of diluents; and in many cases the molecular conformation observed in the crystalline state is also the most stable conformation of the isolated chain. There are also strong correlations between the rates of conformational change for isolated macromolecules in dilute solution and various non‐equilibrium properties of polymeric substances in bulk.During the past decade, great progress has been made in the analysis and prediction of macromolecular conformations. Detailed accounts may be found in the books by VOLKENSTEIN, by BIRSTEIN and PTITSYN, and by FLORY. By combination of several types of experimental evidence with semi‐empirical and theoretical considerations, it has been possible to construct fairly reliable potential energies governing the conformations of a wide variety of chain molecules. An important simplifying feature of the results is that for many purposes it is sufficient to focus attention on the various minima of the potential energy, corresponding to the so‐called rotational‐isomeric states. Another essential feature is that as a rule one finds strong interdependence of the rotational states of adjoining bonds in the chain backbone; a simple example is found in the “pentane effect” for paraffin chains, which renders highly improbable the occurence of two successive gauche rotations of opposite sense. An important exception is seen in polyamides, where the essentially rigid planarity of the amide link allows independence of the rotations of the immediately adjacent bonds. Inclusion of other rigid or semi‐rigid elements in the chain backbone, such as the rings in cellulose and in terephthalate polyesters, leads to similar effects, but in detail each chain is sui generis. The conformations of chains bearing asymmetric centers (e.g., PVC, polypropylene) depends strongly on tacticity and stereoregularity.For the discussion of non‐equilibrium properties at a fundamental level, the maxima (barriers between minima) of the conformational potential energy also play an essential role, but at present most theories of viscoelasticity, for example, are based on less realistic models, such as beads‐and‐springs, random‐flight chain, KRATKY‐POROD wormlike chain, etc. The elaboration of these models and their relation to the detailed molecular structure is currently an active field of study.

Conformational properties of macromolecules with side chain groups. Polycholesterylacrylate

Conformational properties of macromolecules with side chain groups. Polycholesterylacrylate