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Biomedical subjects

A N Semenov

Publications and source records attributed to A N Semenov.

At least 19 recordsLinked to original sources
PubMed2006

Micelle formation in statistical copolymers.

Formation of microdomain structures in concentrated systems of irregular (stochastic) copolymers with weak composition asymmetry (epsilon>>1) is considered theoretically. The study is focused on the weak segregation regime for infinitely long copolymer chains near the disorder-to-order transition. It is shown that the transition occurs below the spinodal (at chi(0)< chi*) and that it results in the formation of micelles rather than in a superposition pattern of a few harmonic composition waves. The micelle size is inversely proportional to Delta(chi=chi)-(chi0). For small Delta(chi) the micelles are like large nearly uniform droplets with "reflected" composition, -epsilon. As Delta(chi) increases the micelle composition profile develops oscillations. A first-order transition from spherical-wave micelles to micelles with internal bcc structure is predicted at chi/chi*-1 proportional to epsilon(2). Interaction of micelles is also considered. It is shown that micelles always tend to form a fcc superlattice. The micellization in the weak segregation regime is controlled by the so-called nonlocal free energy. The classical fourth order (in composition parameter A) approximation for this energy is significantly generalized in the regime of low volume fraction of micelles. It is shown that the nonlocal energy strongly (exponentially) increases with A near and above a certain critical value A approximately equal to A*.

Journal Article↗
PubMed2005

Long-range interactions in polymer melts: the anti-Casimir effect.

It is well known that small neutral particles normally tend to aggregate due to the van der Waals forces. We discover a new universal long-range interaction between solid objects in polymer media that is directly opposite the van der Waals attraction. The new force could reverse the sign of the net interaction, possibly leading to the net repulsion. This universal repulsion comes from the subtracted soft fluctuation modes, which are not present in the real polymer system, but rather are in its ideal counterpart. The predicted effect has a deep relation to the classical Casimir interactions, providing an unusual example of fluctuation-induced repulsion instead of normal attraction. That is why it is referred to as the anti-Casimir effect. We also find that the correlation function of monomer units in a concentrated solution of infinite polymer chains follows a power-law rather than an exponential decay at large distances.

Journal Article↗
PubMed2005

Shape transformations of protein-like copolymer globules.

Shapes of globules formed by amphiphilic multi-block-copolymers in a selective solvent are considered theoretically. We focus on copolymers consisting mostly of insoluble H-units forming large core surrounded by a shell of soluble P-blocks. It is shown that the globule becomes non-spherical when the effective shell tension is low enough. The resultant shape depends on the shell bending energy: it is prolate if this energy is larger than the elastic energy of the core, and oblate in the opposite case. The central result is the prediction of the formation of a surface pattern of fingers accompanying or even preempting the shape transition mentioned above. We elucidate and discuss the following finger morphologies: 1) nearly spherical knob; 2) a necklace of spherical beads extending away from the surface; 3) mostly cylindrical fingers; 4) large thorn-like fingers. The first 3 morphologies develop at equilibrium as the shell area increases (or, equivalently, the shell tension decreases). Considering the relevant kinetical aspects we show that formation of fingers is a nucleation and growth process, and that the energy of their equilibrium nucleation is likely to be high. Therefore, the finger formation may be delayed, and may actually occur in the regime where the plain spherical surface is metastable. It is the last morphology (thorn-like fingers) that characterizes the metastable regimes when the finger formation is controlled by a high activation energy. The universal features of the above predictions inviting experimental tests are discussed.

Computer Simulation↗
PubMed2005

Multimerization: closed or open association scenario?

We address the problem of classification of the type of association (multimerization) in solutions of identical unimers. Although the aggregation is still routinely characterized in terms of either "open association" or "closed association" models, neither of the two models can provide a fair description of many aggregation processes. We demonstrate that a realistic multimerization may show mixed basic features, i.e. simultaneously those typical of the classical open association and those typical of the classical closed association. In particular, we show that a living polymerization may seem to exhibit a critical micelle concentration (CMC), whereas the basic integral characteristics of a "closed" system with rather monodisperse micelles ((m(w)/m(n)(mic) = 1.02) may not imply a well-defined CMC. Therefore, a multimerization must be characterized by the detailed micelle size distribution that largely defines the equilibrium and dynamical properties of the system. To this end, we suggest a simple method of deriving the micelle size distribution c(m) (depending also on the total concentration of amphiphilic molecules) from the concentration dependence of just the mean aggregation number, m(w)(c). Our results thus invite a reconsideration of the basic methods used for interpretation of experimental data on micellization.

Colloids↗
PubMed2004

Long range bond-bond correlations in dense polymer solutions.

The scaling of the bond-bond correlation function P1(s) along linear polymer chains is investigated with respect to the curvilinear distance s along the flexible chain and the monomer density rho via Monte Carlo and molecular dynamics simulations. Surprisingly, the correlations in dense three-dimensional solutions are found to decay with a power law P1(s) approximately s(-omega) with omega=3/2 and the exponential behavior commonly assumed is clearly ruled out for long chains. In semidilute solutions, the density dependent scaling of P1(s) approximately g(-omega(0))(s/g)(-omega) with omega(0)=2-2nu=0.824 (nu=0.588 being Flory's exponent) is set by the number of monomers g(rho) in an excluded volume blob. Our computational findings compare well with simple scaling arguments and perturbation calculation. The power-law behavior is due to self-interactions of chains caused by the chain connectivity and the incompressibility of the melt.

Journal Article↗
PubMed2004

Theoretical notes on dense polymers in two dimensions.

Two models of dense two-dimensional (2d) polymers are considered: (1) when chain intersections in 2d are totally forbidden, and (2) when they are allowed to some extent. It is shown that both polymer chain statistics and dynamics are entirely different for the two models. In the first case studied by Duplantier in 1986 polymer chains are essentially segregated and are characterized by non-classical gamma exponents. The contact line between segregated chains is fractal which leads to an unusual demixing behavior in 2d blends. In the second case (crossings are allowed) polymer coils are overlapping and show mean-field statistics with logarithmic corrections. The correlation function of concentration fluctuations in this system is predicted to exhibit a universal long range power tail (1/r4) which is due to non-mean-field effects. The dynamical behavior of the two models is even more drastically different: The first model is characterized by a relatively fast dynamics with conformational relaxation time tN is proportional to N(15/8) (i.e. tN is slightly shorter than the Rouse time is proportional to N2). On the other hand an exponentially slow dynamics is predicted for model 2 (with 3d entanglements).

Journal Article↗
PubMed2003

Stability of dense hydrophobic-polar copolymer globules: regular, random and designed sequences.

Stability of dense globular structures formed by amphiphilic copolymers consisting of hydrophobic (insoluble) units and a small fraction of single polar (soluble) monomer units is considered in the mean-field approximation for different types of unit distributions along the chain. Polar (P) units are located in a relatively thin surface layer due to their strong repulsion from hydrophobic (H) monomer units. We compared globules formed by different copolymer sequences with the same gross numbers of P- and H-units: regular HP-sequences (P-units separated by equal H-blocks), random copolymers (uncorrelated positions of P-units, i.e. Flory distribution of H-block lengths), proteinlike (PL) sequences (designed sequences involving both long H-blocks dominating by total mass, and short blocks dominating by number). We showed that PL-globules are more stable (lower free energy) and are characterized by a higher temperature of the coil-to-globule transition when compared with the other sequences mentioned above. We also considered HP-H-copolymers consisting of one long and many short hydrophobic blocks; we showed that it is these sequences that yield the dense globules corresponding to the lowest free energy.

Journal Article↗
PubMed2002

Adsorption of a semiflexible wormlike chain.

Adsorption of ideal polymers with stiff backbone onto a flat surface is considered theoretically. Both scaling approach and quantitative theory are developed. We predict a self-similar monomer concentration profile c(x) approximately x(-4/3) near the surface (when the distance to the surface x is much smaller than the chain persistence length l /2). The typical conformation of a weakly adsorbed chain can be viewed as a sequence of alternating flat (2-dimensional) trains of wormlike short loops (flat blobs) and coil-like (3-dimensional) loops forming a triple-layer structure: contact layer (x < Delta) of adsorbed fragments virtually laid on the surface, proximal layer (Delta < x < l) of flat blobs, and more dilute distal corona layer (x > l). Here Delta defines the range of monomer/surface attraction, Delta << l. The adsorption transition is continuous. However, its relative width Delta(T) is divided by T* is small (T(*) is the adsorption temperature, Delta T is the relevant temperature interval): Delta(T) is divided by T* approximately (Delta is divided by l)(4/3), i.e. a discontinuous transition in the limit Delta/ l --> 0.

Journal Article↗
PubMed2001

Hierarchical self-assembly of chiral rod-like molecules as a model for peptide beta -sheet tapes, ribbons, fibrils, and fibers.

A generic statistical mechanical model is presented for the self-assembly of chiral rod-like units, such as beta-sheet-forming peptides, into helical tapes, which with increasing concentration associate into twisted ribbons (double tapes), fibrils (twisted stacks of ribbons), and fibers (entwined fibrils). The finite fibril width and helicity is shown to stem from a competition between the free energy gain from attraction between ribbons and the penalty because of elastic distortion of the intrinsically twisted ribbons on incorporation into a growing fibril. Fibers are stabilized similarly. The behavior of two rationally designed 11-aa residue peptides, P(11)-I and P(11)-II, is illustrative of the proposed scheme. P(11)-I and P(11)-II are designed to adopt the beta-strand conformation and to self-assemble in one dimension to form antiparallel beta-sheet tapes, ribbons, fibrils, and fibers in well-defined solution conditions. The energetic parameters governing self-assembly have been estimated from the experimental data using the model. The 8-nm-wide fibrils consist of eight tapes, are extremely robust (scission energy approximately 200 k(B)T), and sufficiently rigid (persistence length l(fibril) approximately 20-70 microm) to form nematic solutions at peptide concentration c approximately 0.9 mM (volume fraction approximately 0.0009 vol/vol), which convert to self-supporting nematic gels at c > 4 mM. More generally, these observations provide a new insight into the generic self-assembling properties of beta-sheet-forming peptides and shed new light on the factors governing the structures and stability of pathological amyloid fibrils in vivo. The model also provides a prescription of routes to novel macromolecules based on a variety of self-assembling chiral units, and protocols for extraction of the associated energy changes.

Models, Molecular↗
PubMed1999

Dynamics of irregular copolymers.

Reptation dynamics of AB copolymers with irregular chemical structure are considered theoretically. It is shown that interactions between A and B monomers could result in a significant slowdown of copolymer dynamics in the disordered (macroscopically homogeneous) state. The dynamical copolymer length N* showing the crossover to the strongly retarded dynamics is calculated. It is shown that contour-length fluctuations (internal reptation modes) give rise to a strong reduction of the slowdown effect and to a strong increase of N* which becomes unrealistically high in the case of a genuinely random chemical structure. The following scaling dependence of N* is predicted for irregular block copolymers: N* proportional, variant delta(-8)chi(-8)n(-8)(0)N(3)(e), where delta is the degree of block polydispersity, chi the Flory AB interaction parameter, and n(0) the mean block length. The strongest dynamical effect of AB interactions is predicted for correlated random copolymers near the critical point related to the formation of microdomain superstructures.

Journal Article↗
PubMed1996

Theory of gel electrophoresis of DNA: orientational effects.

Some aspects of the reptation model of gel electrophoresis of DNA, with emphasis on the orientational effects, are considered. A master equation for the reptational dynamics with the end boundary conditions is proposed. Based on this equation, the orientation and dynamics of the persistent-chain are investigated. In particular, the role of trap conformations for this chain, which essentially reduce the chain mobility, was analyzed. A transient orientation of the chain during pulsed field gel electrophoresis is also discussed.

DNA↗
PubMed1996

A simple direct enzyme immunoassay of antibodies based on the differences in diffusion rates in a gel of a synthetic antigen and of its complex with antibodies.

A simple direct enzyme immunoassay for semiquantitative detection of antibodies is suggested. It is based on the difference in diffusion rates in a gel for a synthetic low-mol-wt antigen and of its complexes with antibodies to be detected. Sensitivity and specificity of the developed assay are equal to an ELISA method. The assay has been tested with antibodies against HIV protein gp41 in rabbit serum. Possible applications and limitations of the method are discussed.

Animals↗
PubMed1994

Synthesis of the partially protected fragment 1-16 of salmon calcitonin by using the phenylhydrazide protecting group.

The partially protected fragment BOC-Cys(Acm)-Ser(But)-Asn-Leu-Ser(But)-Thr(But)- Cys(Acm)-Val-Leu-Gly-Lys(epsilon-BOC)-Leu-Ser(But)-Glu(OBut)-Leu-O H of salmon calcitonin was synthesized by segment condensation in solution. Segments were synthesized in solution by the DCC/HOBt method using the phenylhydrazide as a semipermanent protecting group for protection of the carboxyl function of the C-terminal residue. The phenylhydrazide protecting group was removed by oxidation with air oxygen catalyzed by copper-pyridine complexes. The segments were then condensed by the DCC/HOBt method according to the scheme (6 + 3) + (3 + 4). The proposed synthetic scheme permits production of gram amounts of the partially protected fragment 1-16 of salmon calcitonin.

Amino Acid Sequence↗
PubMed1994

[Nonproteolytic enzymes for peptide synthesis].

Use of nonproteases in peptide synthesis is reviewed for the first time. The enzymes are suggested to be classified under three groups--ATP-dependent enzymes (not assigned to ribosome system), hydrolases and oxidoreductases.

Adenosine Triphosphate↗
PubMed1993

[Synthesis of a partially purified fragment of salmon calcitonin 1-16 using a phenylhydrazide protective group].

The partially protected fragment Boc-Cys(Acm)-Ser(Bu(t))-Asn-Leu-Ser(Bu(t))-Thr (Bu(t))-Cys(Acm)-Val-Leu-Gly-Lys(Boc)-Leu-Ser(Bu(t))-Gln-Glu(OBu(t ))- Leu-OH of salmon calcitonin was synthesized by the segment condensation in solution. Segments were synthesized by the DCC/HOBt method in solution with phenylhydrazide as a semipermanent protecting group for the carboxyl function of the C-terminal residue. The phenylhydrazide group was removed by oxidation with air oxygen catalyzed by copper pyridine complexes under mild conditions. The segments were then condensed by the DCC/HOBt method according to the scheme (6 + 3) + (3 + 4). The proposed scheme makes it possible to product the partially protected fragment 1-16 of salmon calcitonin on the gram scale.

Amino Acid Sequence↗
PubMed1981

Enzymatic synthesis in biphasic aqueous-organic systems. I. Chemical equilibrium shift.

A theoretical analysis of the causes of chemical equilibrium shift (i.e., change in product yield), accompanying replacement of water as the reaction medium by biphasic system "water-water-immiscible organic solvent", is given. A model is described, which is based on equilibrium partition of reagents between the two phases and establishment of a chemical equilibrium. In terms of this model, the apparent equilibrium constant, Kbiphasic which is evolved from the equilibrium concentrations of the reagents referred to the total volume of the biphasic system, should depend on the ratio of the volume of the organic and aqueous phases and the partition coefficients. The theoretical dependences were verified experimentally. Firstly, it was shown that for oxidation of isobutanol into isobutyraldehyde, catalyzed by alcohol dehydrogenase, the equilibrium shift that takes place in a water-hexane biphasic system is determined by the partition coefficients of the reagents found in an independent experiment. Varying the composition of the organic phase (hexane or ethyl acetate and their mixtures), the equilibrium could be shifted (compared to the aqueous solutions) towards both the initial reagents and the end-products: thereby changing the apparent equilibrium constant by two orders of magnitude. Secondly, alpha-chymotrypsin-catalyzed synthesis of ethyl ester of N-benzoyl-L-phenylalanine (from the respective acid and alcohol) in a biphasic system containing chloroform, benzene, carbon tetrachloride or diethyl ether, has been studied. The apparent equilibrium constant has been experimentally demonstrated to depend on the ratio of the aqueous and organic phase volumes in an extreme fashion, as has been predicted by the theory. The yield of the product in the reaction optimum amounts to 100%, whereas in water it is as low as 0.01%.

Alcohol Oxidoreductases↗