@article {2017,
	title = {Recombination of protein fragments: A promising approach toward engineering proteins with novel nanomechanical properties},
	journal = {Protein Science},
	volume = {17},
	number = {10},
	year = {2008},
	note = {ISI Document Delivery No.: 351CKTimes Cited: 4Cited Reference Count: 50Balamurali, M. M. Sharma, Deepak Chang, Anderson Khor, Dingyue Chu, Ricky Li, Hongbin},
	month = {Oct},
	pages = {1815-1826},
	type = {Article},
	abstract = {Combining single molecule atomic force microscopy (AFM) and protein engineering techniques, here we demonstrate that we can use recombination-based techniques to engineer novel elastomeric proteins by recombining protein fragments from structurally homologous parent proteins. Using I27 and I32 domains from the muscle protein titin as parent template proteins, we systematically shuffled the secondary structural elements of the two parent proteins and engineered 13 hybrid daughter proteins. Although I27 and I32 are highly homologous, and homology modeling predicted that the hybrid daughter proteins fold into structures that are similar to that of parent protein, we found that only eight of the 13 daughter proteins showed beta-sheet dominated structures that are similar to parent proteins, and the other five recombined proteins showed signatures of the formation of significant alpha-helical or random coil-like structure. Single molecule AFM revealed that six recombined daughter proteins are mechanically stable and exhibit mechanical properties that are different from the parent proteins. In contrast, another four of the hybrid proteins were found to be mechanically labile and unfold at forces that are lower than the similar to 20 pN, as we could not detect any unfolding force peaks. The last three hybrid proteins showed interesting duality in their mechanical unfolding behaviors. These results demonstrate the great potential of using recombination-based approaches to engineer novel elastomeric protein domains of diverse mechanical properties. Moreover, our results also revealed the challenges and complexity of developing a recombination-based approach into a laboratory-based directed evolution approach to engineer novel elastomeric proteins.},
	keywords = {ATOMIC-FORCE MICROSCOPY, BIOLOGICAL ROLES, COMPUTATIONAL DESIGN, ELASTICITY, elastomeric protein, EVOLUTION, IMMUNOGLOBULIN DOMAINS, MECHANICAL STABILITY, mechanical unfolding, MOLECULAR-DYNAMICS SIMULATION, recombination, SEQUENCE, SINGLE PROTEIN, single-molecule force spectroscopy, TITIN},
	isbn = {0961-8368},
	url = {<Go to ISI>://000259401900019},
	author = {Balamurali, M. M. and Sharma, D. and Chang, A. and Khor, D. and Chu, R. and Li, H. B.}
}
@article {1291,
	title = {Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers},
	journal = {Biophysical Journal},
	volume = {88},
	number = {1},
	year = {2005},
	note = {ISI Document Delivery No.: 884MYTimes Cited: 36Cited Reference Count: 72},
	month = {Jan},
	pages = {25-36},
	type = {Article},
	abstract = {A detailed molecular dynamics study of the haemagglutinin fusion peptide (N-terminal 20 residues of the HA2 subunits) in a model bilayer has yielded useful information about the molecular interactions leading to insertion into the lipids. Simulations were performed on the native sequence, as well as a number of mutant sequences, which are either fusogenic or nonfusogenic. For the native sequence and fusogenic mutants, the N-terminal 11 residues of the fusion peptides are helical and insert with a tilt angle of similar to30degrees with respect to the membrane normal, in very good agreement with experimental data. The tilted insertion of the native sequence peptide leads to membrane bilayer thinning and the calculated order parameters show larger disorder of the alkyl chains. These results indicate that the lipid packing is perturbed by the fusion peptide and could be used to explain membrane fusion. For the nonfusogenic sequences investigated, it was found that most of them equilibrate parallel to the interface plane and do not adopt a tilted conformation. The presence of a charged residue at the beginning of the sequence (G1E mutant) resulted in a more difficult case, and the outcomes do not fall straightforwardly into the general picture. Sequence searches have revealed similarities of the fusion peptide of influenza haemagglutinin with peptide sequences such as segments of porin, amyloid ab peptide, and a peptide from the prion sequence. These results confirm that the sequence can adopt different folds in different environments. The plasticity and the conformational dependence on the local environment could be used to better understand the function of fusion peptides.},
	keywords = {ANALOGS, CONFORMATION, HEMAGGLUTININ, MEDIATED MEMBRANE-FUSION, MODEL MEMBRANES, MOLECULAR-DYNAMICS SIMULATION, MULTIPLE ALIGNMENT, RECEPTOR-BINDING, SEQUENCE, VIRAL FUSION, VIRUS},
	isbn = {0006-3495},
	url = {<Go to ISI>://000226090900006},
	author = {Vaccaro, L. and Cross, K. J. and Kleinjung, J. and Straus, S. K. and Thomas, D. J. and Wharton, S. A. and Skehel, J. J. and Fraternali, F.}
}
@article {744,
	title = {Assessing the effects of time and spatial averaging in N-15 chemical shift/N-15-H-1 dipolar correlation solid state NMR experiments},
	journal = {Journal of Biomolecular Nmr},
	volume = {26},
	number = {4},
	year = {2003},
	note = {ISI Document Delivery No.: 686MATimes Cited: 30Cited Reference Count: 51},
	month = {Aug},
	pages = {283-295},
	type = {Article},
	abstract = {The effect of time and spatial averaging on N-15 chemical shift/H-1-N-15 dipolar correlation spectra, i.e., PISEMA spectra, of alpha-helical membrane peptides and proteins is investigated. Three types of motion are considered: (a) Librational motion of the peptide planes in the alpha-helix; (b) rotation of the helix about its long axis; and (c) wobble of the helix about a nominal tilt angle. A 2ns molecular dynamics simulation of helix D of bacteriorhodopsin is used to determine the effect of librational motion on the spectral parameters. For the time averaging, the rotation and wobble of this same helix are modelled by assuming either Gaussian motion about the respective angles or a uniform distribution of a given width. For the spatial averaging, regions of possible N-15 chemical shift/H-1-N-15 dipolar splittings are computed for a distribution of rotations and/or tilt angles of the helix. The computed spectra show that under certain motional modes the N-15 chemical shift/H-1-N-15 dipolar pairs for each of the residues do not form patterns which mimic helical wheel patterns. As a result, the unambiguous identification of helix tilt and helix rotation without any resonance assignments or on the basis of a single assignment may be difficult.},
	keywords = {averaging, COAT PROTEIN, GRAMICIDIN CHANNEL, ION-CHANNEL, LIPID BILAYERS, MEMBRANE-PROTEIN STRUCTURE, mobility of membrane helices, MOLECULAR-DYNAMICS SIMULATION, mosaic spread, NUCLEAR-MAGNETIC-RESONANCE, PHOSPHOLIPID-BILAYER, PISA wheels, PISEMA, SPIN-EXCHANGE, time, TRANSMEMBRANE DOMAIN},
	isbn = {0925-2738},
	url = {<Go to ISI>://000183324500001},
	author = {Straus, S. K. and Scott, W. R. P. and Watts, A.}
}
@article {4128,
	title = {Modeling and structure of mercury-water interfaces},
	journal = {Journal of Chemical Physics},
	volume = {107},
	number = {6},
	year = {1997},
	note = {ISI Document Delivery No.: XP280Times Cited: 37Cited Reference Count: 78},
	month = {Aug},
	pages = {2122-2141},
	type = {Article},
	abstract = {The modeling and nature of the physisorption of water at the metal (Hg)-water interface is explored in this paper. We have evaluated potential models that fit into three general classes that are employed in the literature. These classes are distinguished by the manner in which the isotropic interactions between the metal and the water are modeled: namely, as non-attractive, weakly attractive, and strongly attractive. In the present studies the metal is described by a jellium model. In our model, in addition to the isotropic water potential there is an interaction between the jellium and the water molecules which depends on the orientation of the water molecule with respect to the metal surface. We find that hard potentials without isotropic attractive terms dewet. The density of water near hydrocarbon-like potentials remains close to the bulk value but the interaction isn{\textquoteright}t strong enough to structure the water near the interface, nor are the adsorption energies sufficiently high. The strongly attractive potentials seem to be the most appropriate. For such models we have checked the sensitivity of the results to the parameters in our model including surface corrugation. We find that the structural results are insensitive to the parameters employed suggesting that they not only provide a good classical description of the Hg-water interface but may be readily adaptable to describe the physisorption of water on metals in general. Although we find the layering of water molecules and the pattern of hydrogen bonding near these surfaces, which have been described as ice-like in previous studies, the actual arrangement of the water molecules near these surfaces is distinctly different from the structure of ice. (C) 1997 American Institute of Physics.},
	keywords = {CHARGED ELECTRODES, COMPUTER-SIMULATION, DOUBLE-LAYER, ELECTROLYTE, HALIDE-IONS, INTERFACE, LIQUID WATER, METAL INTERFACE, MOLECULAR-DYNAMICS SIMULATION, SURFACE, TIP4P WATER},
	isbn = {0021-9606},
	url = {<Go to ISI>://A1997XP28000045},
	author = {Shelley, J. C. and Patey, G. N. and Berard, D. R. and Torrie, G. M.}
}
@article {3898,
	title = {Structure of the metal aqueous electrolyte solution interface},
	journal = {Journal of Chemical Physics},
	volume = {107},
	number = {12},
	year = {1997},
	note = {ISI Document Delivery No.: XX493Times Cited: 24Cited Reference Count: 47},
	month = {Sep},
	pages = {4719-4728},
	type = {Article},
	abstract = {Theoretical results are given for aqueous electrolyte solutions in contact with uncharged metallic surfaces. The metal is modeled as a jellium slab and is treated using local density functional theory. The solution structure is obtained using the reference hypernetted-chain theory. The two phases interact electrostatically and the coupled theories are iterated to obtain fully self-consistent results for the electron density of the metal and surface-particle correlation functions. The metal-induced structure of pure water and aqueous electrolyte solutions as well as the electrostatic potential drop across the interface are discussed in detail. The results are compared with those for ions in simple dipolar solvents. It is found that the water molecules are ordered by the metal field and that the surface-induced solvent structure strongly influences the ion distributions. (C) 1997 American Institute of Physics.},
	keywords = {CHARGED ELECTRODES, COMPUTER-SIMULATION, ELECTRICAL DOUBLE-LAYER, HALIDE-IONS, INTEGRAL-EQUATION THEORIES, LIQUID WATER, MERCURY-WATER INTERFACE, MOLECULAR-DYNAMICS SIMULATION, PLANAR WALL, SOLVENT MODEL},
	isbn = {0021-9606},
	url = {<Go to ISI>://A1997XX49300029},
	author = {Berard, D. R. and Kinoshita, M. and Cann, N. M. and Patey, G. N.}
}
@article {3809,
	title = {Boundary condition effects in simulations of water confined between planar walls},
	journal = {Molecular Physics},
	volume = {88},
	number = {2},
	year = {1996},
	note = {ISI Document Delivery No.: UN985Times Cited: 86Cited Reference Count: 32},
	month = {Jun},
	pages = {385-398},
	type = {Article},
	abstract = {In computer simulations of water between hydrophobic walls the results exhibit a strong dependence upon the boundary conditions applied. With the minimum image (MI) convention the water molecules tend to be orientationally ordered throughout the simulation cell (Valleau, J. P., and Gardner, A. A., 1987, J. chem. Phys., 86, 4162) whereas, if a spherical cut-off (SC) is applied, strong orientational order is found only in the immediate vicinity of the surface (Lee, C. Y., McCammon, J. A., and Rossky, P. J., 1984, J. chem. Phys., 80, 4448). These conflicting observations have remained unresolved, and clearly raise troubling questions concerning the validity of simulation results for water between surfaces of all types. In the present paper we explore this problem by carrying out a detailed analysis of the results obtained with various types of boundary condition. These include Ewald calculations carried out with a central simulation cell adapted to describe the slab geometry of interest. It is shown that the order observed in MI calculations is an artefact of that particular truncation. The reason for this is isolated and discussed. Similar problems are found if a cylindrical cut-off is employed. The Ewald and SC methods gave qualitatively similar results for systems similar to those considered in previous simulations. However, for some geometries problems can also arise with the SC method. We conclude that in general the slab-adapted Ewald method is the safest choice.},
	keywords = {ADSORPTION, CHARGED ELECTRODES, COMPUTER-SIMULATION, IONS, LIQUID WATER, METAL WALLS, models, MOLECULAR-DYNAMICS SIMULATION, MONTE-CARLO SIMULATIONS, SURFACE},
	isbn = {0026-8976},
	url = {<Go to ISI>://A1996UN98500006},
	author = {Shelley, J. C. and Patey, G. N.}
}
