37 research outputs found
Osmotic pressure induced coupling between cooperativity and stability of a helix-coil transition
Most helix-coil transition theories can be characterized by a set of 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.Comment: 5 pages, 3 figures. To be submitted to Phys.Rev.Let
Water reveals non-Arrhenius kinetics in protein folding experiments
Statistical theories describe systems in equilibrium, and cannot be used to study kinetics. However, the theo-
ries are based on coarse-grained parameters, that include assumptions regarding the underlying kinetics. If
such assumptions are incorrect, the theoretical expressions, used to process the experimental data, will not
fit. I report on one such case we have met within the application of Zimm-Bragg [1] theory to process folding
experiments, and discuss the reasons and consequences.
Studies of relaxation phenomena in glass-forming liquids by default account for the shift in temperature by
some value, corresponding to the glass formation temperature, .In particular, temperature
shift
appears in hydrated proteins because of the presence of partially glassy states giving rise to
non-
Arrhenius relaxation times log Ď„ ~ [2].
A phenomenological approach was suggested
by Adam and Gibbs as early as in 1965 to describe
the sudden increase of viscosity and the slowing down of the collective modes in super-cooled liquids as the
temperature is approaching[3]. The key idea of Adam-Gibbs theory was to consider the supercooled liquid
as a set of clusters (cooperatively rearranging regions) of different sizes that change with temperature,
giving rise to the shift in re-
laxation time. The temperature shift factor is present in many theories
describing properties of water.
Thus, Truskett and Dill had to include the Adamm-Gibbs temperature
shift into their simple analytical model of water to achieve the agreement with experimental data on the tem-
perature dependence of self-diffusion coefficient [4]. Later, Schiro and Weik have summarised recent in vitro
and in silico experimental results regarding the role of hydration water in the onset of protein structural dy-
namics, and have reported the presence of super-Arrhenius relaxation region above the ”protein dynamic
transition” temperature [4]. Recently, Mallamace et al have used the Adam-Gibbs theory in their NMR meas-
urements of protein folding-unfolding in water [4] and to rationalise the complicated pressure-temperature
diagrams in these glass-forming systems.
Motivated by the considerations above, and taking into account the
relationship between the
unimolecular rate of folding in water and the relaxation time 45 , we
introduce the
tem-
perature shift into the formulas used to fit experimental data on hydrated polypeptides.
By doing so we resolve the paradox and complete the new method of processing the Circular Dichroism ex-
perimental data on protein foldin
On spin description of water-biopolymer interactions: theory and experiment of reentrant order-disorder transition.
The experimental studies of biopolymer conformations have reached an unprecedented level of
detailization during the past decade and allow now to study single molecules in vivo [1]. Processing of
experimental data essentially relies on theoretical approaches to conformational transitions in
biopolymers [2]. However, the models that are currently used, originate from the early 1960\u27s and
contain several unjustified assumptions, widely accepted at that time. Thus, the view on the
conformational transitions in the polypeptides as a two-state process has very limited applicability
because the all-or-none transition mechanism takes place only in short polypeptides with sizes
comparable to the spatial correlation lengththe original formulation of Zimm-Bragg model is
phenomenological and does not allow for a microscopic model for waterthe implicit consideration of
the water-polypeptide interactions through the ansatz about the quadratic dependence of free energy
difference on temperature can only be justified through the assumption of an ideal gas with a constant
heat capacity. To get rid of these deficiencies, we augment the Hamiltonian formulation [3] of the
Zimm-Bragg model [4] with the term describing the water-polypeptide interactions [5]. The analytical
solution of the model results in a formula, ready to be fit to Circular Dichroism (CD) data for both heat
and cold denaturation. On the example of several sets of experimental data we show, that our formula
results in a significantly better fit, as compared to the existing approaches. Moreover, the application
of our procedure allows to compare the strengths of inter- and intra-molecular H-bonds, an
information, inaccessible before
Do we really need water models in full, when it comes to studies of biopolymer conformations?
Physics behind the Conformational Transitions in Biopolymers. Demystification of DNA melting and Protein Folding
Biophysics is the area of research, devoted to the studies of physical problems related to living systems. Animal cell is the smallest unit of an organism and mainly contains water solutions of structurally inhomogeneous polymers of biological origin: polypeptides (proteins) and polynucleotides (DNA, RNA). Statistical physics of macromolecules allows to describe the conformations of both synthetic and bio-polymers and constitutes the basis of Biophysics. During the talk I will report on the biophysical problems I have solved with numerical simulations (Langevin-based Molecular Dynamics of Go-like protein folding model and Monte Carlo with Wang-Landau sampling) and analytical studies of spin models (formula evaluation by hand, enforced with computer algebra systems). The direct connections with the theory of phase transitions, algebra of non-commutative operators and decorated spin models will be elucidated