Sh. A. Tonoyan - Academia.edu (original) (raw)
Papers by Sh. A. Tonoyan
Journal of Contemporary Physics (Armenian Academy of Sciences), 2008
Abstract⎯A model is proposed described by a Hamiltonian consisting of two terms corresponding to ... more Abstract⎯A model is proposed described by a Hamiltonian consisting of two terms corresponding to Hamiltonians of the generalized model of polypeptide chain (GMPC) with different scales of interaction. We consider a case where the long-scale interaction corresponds to attraction, while the short-scale interaction corresponds to repulsion; this case models the melting of the system in compact packing conditions (globularized polypeptide or DNA in capsid). In the framework of the transfermatrix approach we calculate the correlation length and the helicity degree. It is shown that the temperature dependence of the correlation length is determined by the complex second eigenvalue of the transfer-matrix. In this regime the system displays a new type of correlations when the melting interval cannot be a measure of the system cooperativity.
Journal of Contemporary Physics (Armenian Academy of Sciences), 2010
Abstract⎯Within the framework of generalized model of polypeptide chain, on the basis of the Hami... more Abstract⎯Within the framework of generalized model of polypeptide chain, on the basis of the Hamiltonian of model of solvent, which interacts with a biopolymer in both competitive and noncompetitive ways, introduced earlier, analytical expressions are obtained and thermodynamic and other averaged parameters are calculated for both the repeating units of the biopolymer and the solvent molecules. Different cases of relations between parameters of competitive and non-competitive bonding are considered and processes of melting and alignment are studied. It is shown that these processes are accompanied by changes in solvation and redistribution of solvent molecules between the helical and coiled portions of the chain.
Journal of Contemporary Physics (Armenian Academy of Sciences), 2013
ABSTRACT The effect of sequence disorder on thermodynamics of ssRNA is studied on the basis of co... more ABSTRACT The effect of sequence disorder on thermodynamics of ssRNA is studied on the basis of constrained annealing approach. A random sequence with bimodal disorder is considered. The temperature behavior of specific heat and helicity degree is examined. A reasonable agreement with numerical results is obtained. In the presence of competing interactions the model exhibits not only partial high-temperature melting, but also partial cold denaturation.
Journal of Contemporary Physics-Armenian Academy of Sciences, 2009
Abstract On the basis of generalized model of polypeptide chain (GMPC) as a microscopic theory o... more Abstract On the basis of generalized model of polypeptide chain (GMPC) as a microscopic theory of the helix-coil transition applicable to both polypeptides and DNA, the Hamiltonian of the model of solvent, which interacts with a biopolymer in both competitive and non-competitive ways, is introduced. It is shown that the partition function of this model is reduced to multipliers to the model without solvent. In this case thermal and entropic parameters of the theory are redefined. Based on calculation of the helicity degree and correlation length different cases of relation between parameters of competitive and non-competitive interaction are discussed.
Physical Review Letters, 2012
Most helix-coil transition theories can be characterized by three parameters: energetic, describi... more Most helix-coil transition theories can be characterized by three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to the helical state formation; and geometric, indicating how many repeating units are affected by the formation of one helical state. Depending on their effect on the helix-coil transition, solvents or co-solutes can be classified with respect to their action on these parameters. Solvent interactions that alter the entropic cost of helix formation by their osmotic action can affect both the stability (transition temperature) and the cooperativity (transition interval) of the helix-coil transition. A consistent inclusion of osmotic pressure effects in a description of helix-coil transition, for poly(L-glutamic acid) in solution with polyethylene glycol, can offer an explanation of the experimentally observed linear dependence of transition temperature on osmotic pressure as well as the concurrent changes in the cooperativity of the transition.
Physical Review E, 2014
We analyze the problem of the helix-coil transition in explicit solvents analytically by using sp... more We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer hydrogen bonds that can compete with the intrinsic intra-polymer hydrogen bonded configurations (competing interactions) and implicit solvent action, where the solvent-polymer interactions tune biopolymer configurations by changing the activity of the solvent (non-competing interactions). The overall spin Hamiltonian is comprised of three terms: the background in vacuo Hamiltonian of the "Generalized Model of Polypeptide Chain" type and two additive terms that account for the two above mechanisms of solvent action. We show that on this level the solvent degrees of freedom can be explicitly and exactly traced over, the ensuing effective partition function combining all the solvent effects in a unified framework. In this way we are able to address helix-coil transitions for polypeptides, proteins, and DNA, with different buffers and different external constraints. Our spin-based effective Hamiltonian is applicable for treatment of such diverse phenomena as cold denaturation, effects of osmotic pressure on the cold and warm denaturation, complicated temperature dependence of the hydrophobic effect as well as providing a conceptual base for understanding the behavior of intrinsically disordered proteins and their analogues.
The Journal of Chemical Physics, 2009
The generalized model of polypeptide chains is extended to describe the helix-coil transition in ... more The generalized model of polypeptide chains is extended to describe the helix-coil transition in a system comprised of two chains interacting side-by-side. The Hamiltonian of the model takes into account four possible types of interactions between repeated units of the two chains, i.e., helix-helix, helix-coil, coil-helix, and coil-coil. Analysis reveals when the energy I(hh)+I(cc) of (h-h, c-c) interactions overwhelms the energy I(hc)+I(ch) of mixed (h-c, c-h) interactions, the correlation length rises substantially, resulting in narrowing of the transition interval. In the opposite case, when I(hh)+I(cc)<I(hc)+I(ch), nontrivial behavior of the system is predicted where an intermediate plateau appears on the denaturation curve. For the latter case, calculations of the number of junctions and the average length of helical segments indicate rearrangement of helical segments at the transition point. Conceptual links are established with experimentally oriented theories of Ghosh and Dill [J. Am. Chem. Soc. 131, 2306 (2009)] and Skolnick and Holtzer [Biochemistry 25, 6192 (1986)], providing a potential explanation for both favorable helix formation and disfavored intersegment interactions from the same theoretical perspective.
The Journal of Chemical Physics, 2008
The generalized model of polypeptide chains (GMPC) is expanded to simultaneously consider two typ... more The generalized model of polypeptide chains (GMPC) is expanded to simultaneously consider two types of interactions occurring over different scales. This new two scale GMPC is applied in several specific cases to examine: The combined influence of stacking or antistacking and hydrogen bonding, or spatial restrictions on the length of helical segments, on the cooperativity and temperature interval of the helix-coil transition of duplex DNA. For the cases of stacking or antistacking in combination with hydrogen bonding the model reduces to the basic uniscale model with a redefined scaling parameter Delta. Antistacking increases the cooperativity, while stacking decreases it. In each case, explanations are given in terms of different lengths of helical segments. Restrictions on the length of helical regions result in the appearance of antiferromagnetic-type correlations where there is no apparent link between cooperativity and transition interval.
Physical Review E, 2011
The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with th... more The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds.
Journal of Contemporary Physics (Armenian Academy of Sciences), 2008
Abstract⎯A model is proposed described by a Hamiltonian consisting of two terms corresponding to ... more Abstract⎯A model is proposed described by a Hamiltonian consisting of two terms corresponding to Hamiltonians of the generalized model of polypeptide chain (GMPC) with different scales of interaction. We consider a case where the long-scale interaction corresponds to attraction, while the short-scale interaction corresponds to repulsion; this case models the melting of the system in compact packing conditions (globularized polypeptide or DNA in capsid). In the framework of the transfermatrix approach we calculate the correlation length and the helicity degree. It is shown that the temperature dependence of the correlation length is determined by the complex second eigenvalue of the transfer-matrix. In this regime the system displays a new type of correlations when the melting interval cannot be a measure of the system cooperativity.
Journal of Contemporary Physics (Armenian Academy of Sciences), 2010
Abstract⎯Within the framework of generalized model of polypeptide chain, on the basis of the Hami... more Abstract⎯Within the framework of generalized model of polypeptide chain, on the basis of the Hamiltonian of model of solvent, which interacts with a biopolymer in both competitive and noncompetitive ways, introduced earlier, analytical expressions are obtained and thermodynamic and other averaged parameters are calculated for both the repeating units of the biopolymer and the solvent molecules. Different cases of relations between parameters of competitive and non-competitive bonding are considered and processes of melting and alignment are studied. It is shown that these processes are accompanied by changes in solvation and redistribution of solvent molecules between the helical and coiled portions of the chain.
Journal of Contemporary Physics (Armenian Academy of Sciences), 2013
ABSTRACT The effect of sequence disorder on thermodynamics of ssRNA is studied on the basis of co... more ABSTRACT The effect of sequence disorder on thermodynamics of ssRNA is studied on the basis of constrained annealing approach. A random sequence with bimodal disorder is considered. The temperature behavior of specific heat and helicity degree is examined. A reasonable agreement with numerical results is obtained. In the presence of competing interactions the model exhibits not only partial high-temperature melting, but also partial cold denaturation.
Journal of Contemporary Physics-Armenian Academy of Sciences, 2009
Abstract On the basis of generalized model of polypeptide chain (GMPC) as a microscopic theory o... more Abstract On the basis of generalized model of polypeptide chain (GMPC) as a microscopic theory of the helix-coil transition applicable to both polypeptides and DNA, the Hamiltonian of the model of solvent, which interacts with a biopolymer in both competitive and non-competitive ways, is introduced. It is shown that the partition function of this model is reduced to multipliers to the model without solvent. In this case thermal and entropic parameters of the theory are redefined. Based on calculation of the helicity degree and correlation length different cases of relation between parameters of competitive and non-competitive interaction are discussed.
Physical Review Letters, 2012
Most helix-coil transition theories can be characterized by three parameters: energetic, describi... more Most helix-coil transition theories can be characterized by three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to the helical state formation; and geometric, indicating how many repeating units are affected by the formation of one helical state. Depending on their effect on the helix-coil transition, solvents or co-solutes can be classified with respect to their action on these parameters. Solvent interactions that alter the entropic cost of helix formation by their osmotic action can affect both the stability (transition temperature) and the cooperativity (transition interval) of the helix-coil transition. A consistent inclusion of osmotic pressure effects in a description of helix-coil transition, for poly(L-glutamic acid) in solution with polyethylene glycol, can offer an explanation of the experimentally observed linear dependence of transition temperature on osmotic pressure as well as the concurrent changes in the cooperativity of the transition.
Physical Review E, 2014
We analyze the problem of the helix-coil transition in explicit solvents analytically by using sp... more We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer hydrogen bonds that can compete with the intrinsic intra-polymer hydrogen bonded configurations (competing interactions) and implicit solvent action, where the solvent-polymer interactions tune biopolymer configurations by changing the activity of the solvent (non-competing interactions). The overall spin Hamiltonian is comprised of three terms: the background in vacuo Hamiltonian of the &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot;Generalized Model of Polypeptide Chain&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;quot; type and two additive terms that account for the two above mechanisms of solvent action. We show that on this level the solvent degrees of freedom can be explicitly and exactly traced over, the ensuing effective partition function combining all the solvent effects in a unified framework. In this way we are able to address helix-coil transitions for polypeptides, proteins, and DNA, with different buffers and different external constraints. Our spin-based effective Hamiltonian is applicable for treatment of such diverse phenomena as cold denaturation, effects of osmotic pressure on the cold and warm denaturation, complicated temperature dependence of the hydrophobic effect as well as providing a conceptual base for understanding the behavior of intrinsically disordered proteins and their analogues.
The Journal of Chemical Physics, 2009
The generalized model of polypeptide chains is extended to describe the helix-coil transition in ... more The generalized model of polypeptide chains is extended to describe the helix-coil transition in a system comprised of two chains interacting side-by-side. The Hamiltonian of the model takes into account four possible types of interactions between repeated units of the two chains, i.e., helix-helix, helix-coil, coil-helix, and coil-coil. Analysis reveals when the energy I(hh)+I(cc) of (h-h, c-c) interactions overwhelms the energy I(hc)+I(ch) of mixed (h-c, c-h) interactions, the correlation length rises substantially, resulting in narrowing of the transition interval. In the opposite case, when I(hh)+I(cc)<I(hc)+I(ch), nontrivial behavior of the system is predicted where an intermediate plateau appears on the denaturation curve. For the latter case, calculations of the number of junctions and the average length of helical segments indicate rearrangement of helical segments at the transition point. Conceptual links are established with experimentally oriented theories of Ghosh and Dill [J. Am. Chem. Soc. 131, 2306 (2009)] and Skolnick and Holtzer [Biochemistry 25, 6192 (1986)], providing a potential explanation for both favorable helix formation and disfavored intersegment interactions from the same theoretical perspective.
The Journal of Chemical Physics, 2008
The generalized model of polypeptide chains (GMPC) is expanded to simultaneously consider two typ... more The generalized model of polypeptide chains (GMPC) is expanded to simultaneously consider two types of interactions occurring over different scales. This new two scale GMPC is applied in several specific cases to examine: The combined influence of stacking or antistacking and hydrogen bonding, or spatial restrictions on the length of helical segments, on the cooperativity and temperature interval of the helix-coil transition of duplex DNA. For the cases of stacking or antistacking in combination with hydrogen bonding the model reduces to the basic uniscale model with a redefined scaling parameter Delta. Antistacking increases the cooperativity, while stacking decreases it. In each case, explanations are given in terms of different lengths of helical segments. Restrictions on the length of helical regions result in the appearance of antiferromagnetic-type correlations where there is no apparent link between cooperativity and transition interval.
Physical Review E, 2011
The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with th... more The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds.