@article {2149,
	title = {Configurational entropy modulates the mechanical stability of protein GB1},
	journal = {Journal of Molecular Biology},
	volume = {379},
	number = {4},
	year = {2008},
	note = {ISI Document Delivery No.: 314NITimes Cited: 10Cited Reference Count: 39Li, Hongbin Wang, Hui-Chuan Cao, Yi Sharma, Deepak Wang, Meijia},
	month = {Jun},
	pages = {871-880},
	type = {Article},
	abstract = {Configurational entropy plays important roles in defining the thermodynamic stability as well as the folding/unfolding kinetics of proteins. Here we combine single-molecule atomic force microscopy and protein engineering techniques to directly examine the role of configurational entropy in the mechanical unfolding kinetics and mechanical stability of proteins. We used a small protein, GB1, as a model system and constructed four mutants that elongate loop 2 of GB1 by 2, 5, 24 and 46 flexible residues, respectively. These loop elongation mutants fold properly as determined by far-UV circular dichroism spectroscopy, suggesting that loop 2 is well tolerant of loop insertions without affecting GB1{\textquoteright}s native structure. Our single-molecule atomic force microscopy results reveal that loop elongation decreases the mechanical stability of GB1 and accelerates the mechanical unfolding kinetics. These results can be explained by the loss of configurational entropy upon closing an unstructured flexible loop using classical polymer theory, highlighting the important role of loop regions in the mechanical unfolding of proteins. This study not only demonstrates a general approach to investigating the structural deformation of the loop regions in mechanical unfolding transition state, but also provides the foundation to use configurational entropy as an effective means to modulate the mechanical stability of proteins, which is of critical importance towards engineering artificial elastomeric proteins with tailored nanomechanical properties. (C) 2008 Elsevier Ltd. All rights reserved.},
	keywords = {configurational entropy, DISULFIDE BONDS, FORCE, FORCE SPECTROSCOPY, FRAGMENT RECONSTITUTION, IMMUNOGLOBULIN BINDING DOMAIN, length, LOOP, MECHANICAL STABILITY, mechanical unfolding, MODULES, resistance, single molecule atomic force microscopy, SINGLE PROTEIN, SPECTROSCOPY, TITIN, TRANSITION-STATE},
	isbn = {0022-2836},
	url = {<Go to ISI>://000256815700018},
	author = {Li, H. B. and Wang, H. C. and Cao, Y. and Sharma, D. and Wang, M.}
}
@article {2218,
	title = {Hydrophobic interactions in urea - Trimethylamine-N-oxide solutions},
	journal = {Journal of Physical Chemistry B},
	volume = {112},
	number = {35},
	year = {2008},
	note = {ISI Document Delivery No.: 342RDTimes Cited: 2Cited Reference Count: 25Paul, Sandip Patey, G. N.},
	month = {Sep},
	pages = {11106-11111},
	type = {Article},
	abstract = {The influence of osmolytes urea and trimethylemine-N-oxide (TMAO) on hydrophobic interactions is investigated employing molecular dynamics simulations. These osmolytes are of interest because of their opposing influence on proteins in solution; the denaturing effect of urea can be countered with TMAO. A neopentane pair is used to model typical nonpolar entities. Binary water-urea and water-TMAO as well as ternary water-urea-TMAO systems are considered. Neopentane-neopentane potentials of mean force, neopentane-water, and neopentane-osmolyte distribution functions are reported. Urea is found to have only modest influence on the neopentane-neopentane potential of mean force, but the hydrophobic attraction is completely destroyed by the presence of TMAO. It is shown that TMAO tends to act as a simple "surfactant" displacing water and urea (if it is present) from the first solvation shell of neopentane. It is likely the surfactant-like influence of TMAO that accounts for the elimination of the hydrophobic attraction. The implications of Our results for explanations of the action of TMAO in protein solutions are discussed.},
	keywords = {AQUEOUS UREA, FORCE, MOLECULAR-DYNAMICS, OSMOLYTES, POTENTIALS, PROTEIN DENATURATION, SIMULATIONS, WATER},
	isbn = {1520-6106},
	url = {<Go to ISI>://000258800300046},
	author = {Paul, S. and Patey, G. N.}
}
@article {1163,
	title = {First passage times of driven DNA hairpin unzipping},
	journal = {Physical Biology},
	volume = {2},
	number = {3},
	year = {2005},
	note = {ISI Document Delivery No.: 007TLTimes Cited: 11Cited Reference Count: 25},
	month = {Sep},
	pages = {166-174},
	type = {Article},
	abstract = {We model the dynamics of voltage-driven transport of DNA hairpins through transmembrane channels. A two-dimensional stochastic model of the DNA translocation process is fit to the measurements of Mathe, who pulled self-hybridized DNA hairpins through lipid-embedded alpha-hemolysin channels. As the channel was too narrow to accommodate hybridized DNA, dehybridization of the hairpin became the rate-limiting step of the transport process. We show that the mean first passage time versus voltage curve for the escape of the DNA from the transmembrane channel can be divided into two regions: (1) a low-voltage region where the DNA slides out of the pore in reverse and without undergoing significant dehybridization, and (2) a region where the DNA dehybridizes under the influence of the applied voltage and translocates across the membrane.},
	keywords = {CHANNEL, DYNAMICS, FORCE, MEMBRANE, MOLECULES, NANOPORE, POLYMER TRANSLOCATION, PORE, SEQUENCE},
	isbn = {1478-3967},
	url = {<Go to ISI>://000234992600006},
	author = {Lakatos, G. and Chou, T. and Bergersen, B. and Patey, G. N.}
}
@article {4895,
	title = {Forces between like-charged walls in an electrolyte solution: A comparison of McMillan-Mayer results for several models},
	journal = {Journal of Chemical Physics},
	volume = {113},
	number = {7},
	year = {2000},
	note = {ISI Document Delivery No.: 344XYTimes Cited: 8Cited Reference Count: 28},
	month = {Aug},
	pages = {2851-2855},
	type = {Article},
	abstract = {The interaction of like-charged walls immersed in aqueous solutions with monovalent counterions is investigated at the McMillan-Mayer (MM) level of description. The net pressure acting between the walls is obtained by applying the anisotropic hypernetted-chain theory. The MM approach requires solvent-averaged ion-ion potentials of mean force as input. Results based on "realistic" models for Na+ and Cl- in water are available in the literature and these are used in the present calculations. The wall-wall interactions obtained can differ dramatically from the primitive model (dielectric continuum solvent) case. For some models attractive wall-wall forces are observed at small separations. The MM theory is found to be rather sensitive to details of the counterion-counterion potential of mean force, and different models for the same counterion can give qualitatively different results. At present it is difficult to evaluate the relative accuracy of the different models that have been proposed. However, the results presented here give at least an idea of the interesting possibilities that lie in the physically realistic range. (C) 2000 American Institute of Physics. [S0021-9606(00)50331-6].},
	keywords = {APPROXIMATION, DOUBLE-LAYER, FORCE, HARD-SPHERES, IMAGE INTERACTIONS, INHOMOGENEOUS COULOMB FLUIDS, MEAN, MOLECULAR-DYNAMICS, PLANAR SURFACES, SODIUM-CHLORIDE, WATER},
	isbn = {0021-9606},
	url = {<Go to ISI>://000088787400034},
	author = {Otto, F. and Patey, G. N.}
}
@article {7131,
	title = {ACTIVITY-COEFFICIENTS OF MODEL AQUEOUS-ELECTROLYTE SOLUTIONS - SENSITIVITY TO THE SHORT-RANGE PART OF THE INTERIONIC POTENTIAL},
	journal = {Journal of Chemical Physics},
	volume = {94},
	number = {10},
	year = {1991},
	note = {ISI Document Delivery No.: FL001Times Cited: 7Cited Reference Count: 12},
	month = {May},
	pages = {6782-6783},
	type = {Article},
	abstract = {Activity coefficients are calculated for model aqueous alkali halide solutions. The theoretical results are found to be very sensitive to details of the interionic potential employed and good agreement with experiment is obtained by simply superimposing an additional r-n repulsive interaction upon charged hard sphere potentials. The "best fits" to the experimental data involve interesting changes in the solution structure. In particular, our results suggest that the strong deviations from limiting behavior observed for some alkali halide solutions (e.g., NaCl) are closely associated with structures involving solvent separated as opposed to contact ion pairs.},
	keywords = {EXTENDED RISM EQUATION, FORCE, INFINITE DILUTION, MEAN, MOLECULAR THEORY, SOLVENT},
	isbn = {0021-9606},
	url = {<Go to ISI>://A1991FL00100046},
	author = {Ursenbach, C. P. and Wei, D. Q. and Patey, G. N.}
}
