arXiv subjects

D. B. Lukatsky

Publications and source records attributed to D. B. Lukatsky.

7 recordsLinked to original sources

arXiv2006

Structural similarity enhances interaction propensity of proteins

We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar structures. The effects originate in the fact that the probability to find a pattern self-match between two identical, even randomly organized interacting protein surfaces is always higher compared with the probability for a pattern match between two different, promiscuous protein surfaces. This theoretical finding explains statistical prevalence of homodimers in protein-protein interaction networks reported earlier. Further, our findings are confirmed by the analysis of curated database of protein complexes that showed highly statistically significant overrepresentation of dimers formed by structurally similar proteins with highly divergent sequences (superfamily heterodimers). We predict that significant fraction of heterodimers evolved from homodimers with the negative design evolutionary pressure applied against promiscuous homodimer formation. This is achieved through the formation of highly specific contacts formed by charged residues as demonstrated both in model and real superfamily heterodimers

q-bio.BM↗

arXiv2006

Statistically enhanced self-attraction of random patterns

In this work we develop a theory of interaction of randomly patterned surfaces as a generic prototype model of protein-protein interactions. The theory predicts that pairs of randomly superimposed identical (homodimeric) random patterns have always twice as large magnitude of the energy fluctuations with respect to their mutual orientation, as compared with pairs of different (heterodimeric) random patterns. The amplitude of the energy fluctuations is proportional to the square of the average pattern density, to the square of the amplitude of the potential and its characteristic length, and scales linearly with the area of surfaces. The greater dispersion of interaction energies in the ensemble of homodimers implies that strongly attractive complexes of random surfaces are much more likely to be homodimers, rather than heterodimers. Our findings suggest a plausible physical reason for the anomalously high fraction of homodimers observed in real protein interaction networks.

q-bio.BM↗

arXiv2004

Multiple stalk formation as a pathway of defect-induced membrane fusion

We propose that the first stage of membrane fusion need not be the formation of a single stalk. Instead, we consider a scenario for defect-induced membrane fusion that proceeds cooperatively via multiple stalk formation. The defects (stalks or pores) attract each other via membrane-mediated capillary interactions that result in a condensation transition of the defects. The resulting dense phase of stalks corresponds to the so-called fusion intermediate.

cond-mat.soft↗

arXiv2004

Phase Behavior and Selectivity of DNA-linked Nanoparticle Assemblies

We propose a model that can account for the experimentally observed phase behavior of DNA-nanoparticle assemblies (R. Jin et al., JACS 125, 1643 (2003); T. A. Taton et al., Science 289, 1757 (2000)). The binding of DNA-coated nano-particles by dissolved DNA linker can be described by exploiting an analogy with quantum particles obeying fractional statistics. In accordance with experimental findings, we predict that the phase-separation temperature of the nano-colloids increases with the DNA coverage of the colloidal surface. Upon the addition of salt, the demixing temperature increases logarithmically with the salt concentration. Our analysis suggests an experimental strategy to map microscopic DNA sequences onto the macroscopic phase behavior of the DNA-nanoparticle solutions. Such an approach should enhance the efficiency of methods to detect (single) mutations in specific DNA sequences.

cond-mat.soft↗

arXiv2003

Slow fluctuations in enhanced Raman scattering and surface roughness relaxation

We propose an explanation for the recently measured slow fluctuations and ``blinking'' in the surface enhanced Raman scattering (SERS) spectrum of single molecules adsorbed on a silver colloidal particle. We suggest that these fluctuations may be related to the dynamic relaxation of the surface roughness on the nanometer scale and show that there are two classes of roughness with qualitatively different dynamics. The predictions agree with measurements of surface roughness relaxation. Using a theoretical model for the kinetics of surface roughness relaxation in the presence of charges and optical electrical fields, we predict that the high-frequency electromagnetic field increases both the effective surface tension and the surface diffusion constant and thus accelerates the surface smoothing kinetics and time scale of the Raman fluctuations in manner that is linear with the laser power intensity, while the addition of salt retards the surface relaxation kinetics and increases the time scale of the fluctuations. These predictions are in qualitative agreement with the Raman experiments.

cond-mat.soft↗

arXiv2002

Universal reduction of pressure between charged surfaces by long-wavelength surface charge modulation

We predict theoretically that long-wavelength surface charge modulations universally reduce the pressure between the charged surfaces with counterions compared with the case of uniformly charged surfaces with the same average surface charge density. The physical origin of this effect is the fact that surface charge modulations always lead to enhanced counterion localization near the surfaces, and hence, fewer charges at the midplane. We confirm the last prediction with Monte Carlo simulations.

cond-mat.soft↗

arXiv2002

Charge Fluctuations and Counterion Condensation

We predict a condensation phenomenon in an overall neutral system, consisting of a single charged plate and its oppositely charged counterions. Based on the ``two-fluid'' model, in which the counterions are divided into a ``free'' and a ``condensed'' fraction, we argue that for high surface charge, fluctuations can lead to a phase transition in which a large fraction of counterions is condensed. Furthermore, we show that depending on the valence, the condensation is either a first-order or a smooth transition.

cond-mat.soft↗