--- trunk/langevin/langevin.bib 2008/01/23 22:36:36 3332 +++ trunk/langevin/langevin.bib 2008/01/24 14:16:07 3333 @@ -2,15 +2,164 @@ %% http://bibdesk.sourceforge.net/ -%% Created for Dan Gezelter at 2008-01-11 16:20:18 -0500 +%% Created for Dan Gezelter at 2008-01-22 11:01:35 -0500 %% Saved with string encoding Western (ASCII) + +@string{acp = {Adv. Chem. Phys.}} + +@string{ccp5 = {CCP5 Information Quarterly}} + +@string{cp = {Chem. Phys.}} + +@string{cpl = {Chem. Phys. Lett.}} + +@string{jacs = {J. Am. Chem. Soc.}} + +@string{jcc = {J. Comp. Chem.}} + +@string{jcop = {J. Comp. Phys.}} + +@string{jcp = {J. Chem. Phys.}} + +@string{jml = {J. Mol. Liq.}} + +@string{jpc = {J. Phys. Chem.}} + +@string{jpca = {J. Phys. Chem. A}} + +@string{jpcb = {J. Phys. Chem. B}} + +@string{mp = {Mol. Phys.}} + +@string{pams = {Proc. Am. Math Soc.}} + +@string{pccp = {Phys. Chem. Chem. Phys.}} + +@string{pnas = {Proc. Natl. Acad. Sci. USA}} + +@string{pr = {Phys. Rev.}} + +@string{pra = {Phys. Rev. A}} + +@string{prb = {Phys. Rev. B}} + +@string{pre = {Phys. Rev. E}} + +@string{prl = {Phys. Rev. Lett.}} + +@string{rmp = {Rev. Mod. Phys.}} + + +@misc{Chun:2000fj, + Abstract = {A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. (C) 2000 John Wiley \& Sons, Inc.}, + Author = {Chun, HM and Padilla, CE and Chin, DN and Watanabe, M and Karlov, VI and Alper, HE and Soosaar, K and Blair, KB and Becker, OM and Caves, LSD and Nagle, R and Haney, DN and Farmer, BL}, + Date-Added = {2008-01-22 10:38:33 -0500}, + Date-Modified = {2008-01-22 10:38:49 -0500}, + Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators}, + Note = {Journal of Computational Chemistry}, + Pages = {159-184}, + Timescited = {0}, + Title = {MBO(N)D: A multibody method for long-time molecular dynamics simulations}, + Volume = {21}, + Year = {2000}} + +@article{Fogolari:1996lr, + Abstract = {In an effort to reduce the number of degrees of freedom necessary to describe a polypeptide chain we analyze the statistical behavior of polypeptide chains when represented as C alpha chains, C alpha chains with C beta atoms attached, and C alpha chains with rotational ellipsoids as models of side chains. A statistical analysis on a restricted data set of 75 unrelated protein structures is performed. The comparison of the database distributions with those obtained by model calculation on very short polypeptide stretches allows the dissection of local versus nonlocal features of the distributions. The database distribution of the bend angles of polypeptide chains of pseudo bonded C alpha atoms spans a restricted range of values and shows a bimodal structure. On the other hand, the torsion angles of the C alpha chain may assume almost all possible values. The distribution is bimodal, but with a much broader probability distribution than for bend angles. The C alpha - C beta vectors may be taken as representative of the orientation of the lateral chain, as the direction of the bond is close to the direction of the vector joining C alpha to the ad hoc defined center of the "steric mass" of the side chain. Interestingly, both the bend angle defined by C alpha i-C alpha i+1-C beta i+1 and the torsional angle offset of the pseudo-dihedral C alpha i-C alpha i+1-C alpha i+2-C beta i+2 with respect to C alpha i-C alpha i+1-C alpha i+2-C alpha i+3 span a limited range of values. The latter results show that it is possible to give a more realistic representation of polypeptide chains without introducing additional degrees of freedom, i.e., by just adding to the C alpha chain a C beta with given side-chain properties. However, a more realistic description of side chains may be attained by modeling side chains as rotational ellipsoids that have roughly the same orientation and steric hindrance. To this end, we define the steric mass of an atom as proportional to its van der Waals volume and we calculate the side-chain inertia ellipsoid assuming that the steric mass of each atom is uniformly distributed within its van der Waals volume. Finally, we define the rotational ellipsoid representing the side chain as the uniform density ellipsoid possessing the same rotationally averaged inertia tensor of the side chain. The statistics of ellipsoid parameters support the possibility of representing a side chain via an ellipsoid, independently of the local conformation. To make this description useful for molecular modeling we describe ellipsoid-ellipsoid interactions via a Lennard-Jones potential that preserves the repulsive core of the interacting ellipsoids and takes into account their mutual orientation. Tests are performed for two different forms of the interaction potential on a set of high-resolution protein structures. Results are encouraging, in view of the drastic simplifications that were introduced.}, + Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.}, + Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S}, + Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S}, + Da = {19960924}, + Date-Added = {2008-01-22 10:19:04 -0500}, + Date-Modified = {2008-01-22 10:19:09 -0500}, + Dcom = {19960924}, + Edat = {1996/03/01}, + Issn = {0006-3495 (Print)}, + Jid = {0370626}, + Journal = {Biophys J}, + Jt = {Biophysical journal}, + Language = {eng}, + Lr = {20071115}, + Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; *Models, Molecular; Molecular Structure; Peptides/*chemistry; *Protein Conformation; Software; Thermodynamics}, + Mhda = {1996/03/01 00:01}, + Number = {3}, + Own = {NLM}, + Pages = {1183--1197}, + Pl = {UNITED STATES}, + Pmid = {8785277}, + Pst = {ppublish}, + Pt = {Journal Article}, + Pubm = {Print}, + Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)}, + Sb = {IM}, + So = {Biophys J. 1996 Mar;70(3):1183-97. }, + Stat = {MEDLINE}, + Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.}, + Volume = {70}, + Year = {1996}} + +@inbook{Ramachandran1996, + Address = {Providence, Rhode Island}, + Author = {GOMATHI RAMACHANDRAN AND TAMAR SCHLICK}, + Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model}, + Date-Added = {2008-01-22 10:03:42 -0500}, + Date-Modified = {2008-01-22 10:06:57 -0500}, + Editor = {P. M. Pardalos and D. Shalloway and G. Xue}, + Pages = {215-231}, + Publisher = {American Mathematical Society}, + Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science}, + Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding}, + Volume = {23}, + Year = {1996}} + +@article{FIXMAN:1986lr, + Author = {FIXMAN, M}, + Date-Added = {2008-01-22 09:59:29 -0500}, + Date-Modified = {2008-01-22 09:59:35 -0500}, + Journal = {Macromolecules}, + Pages = {1204-1207}, + Timescited = {0}, + Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION}, + Volume = {19}, + Year = {1986}} + +@article{Berendsen87, + Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma}, + Date-Added = {2008-01-22 09:53:15 -0500}, + Date-Modified = {2008-01-22 09:53:15 -0500}, + Journal = jpc, + Pages = {6269-6271}, + Title = {The Missing Term in Effective Pair Potentials}, + Volume = 91, + Year = 1987} + +@incollection{Berendsen81, + Address = {Dordrecht}, + Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans}, + Booktitle = {Intermolecular Forces}, + Date-Added = {2008-01-22 09:52:49 -0500}, + Date-Modified = {2008-01-22 09:52:49 -0500}, + Editor = {B. Pullman}, + Pages = {331-342}, + Publisher = {Reidel}, + Title = {Simple Point Charge Water}, + Year = 1981} +@article{Stillinger74, + Author = {F.~H. Stillinger and A. Rahman}, + Date-Added = {2008-01-22 09:51:43 -0500}, + Date-Modified = {2008-01-22 09:51:43 -0500}, + Journal = jcp, + Number = 4, + Pages = {1545-1557}, + Title = {Improved simulation of liquid water by molecular dynamics}, + Volume = 60, + Year = 1974} @article{Torre:1983lr, - Author = {de la Torre, Jose Garcia and Rodes, Vicente}, + Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente}, Date-Added = {2008-01-11 16:16:43 -0500}, Date-Modified = {2008-01-11 16:16:43 -0500}, Journal = {The Journal of Chemical Physics}, @@ -24,7 +173,8 @@ Ty = {JOUR}, Url = {http://link.aip.org/link/?JCP/79/2454/1}, Volume = 79, - Year = 1983} + Year = 1983, + Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}} @article{PhysRev.119.53, Author = {Favro, L. Dale}, @@ -39,7 +189,8 @@ Publisher = {American Physical Society}, Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body}, Volume = 119, - Year = 1960} + Year = 1960, + Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}} @article{hess:209, Author = {Berk Hess}, @@ -54,13 +205,15 @@ Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations}, Url = {http://link.aip.org/link/?JCP/116/209/1}, Volume = 116, - Year = 2002} + Year = 2002, + Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1}, + Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}} @article{Garcia-de-la-Torre:1997qy, Abstract = {Single-valued hydrodynamic coefficients of a rigid particle can be calculated from existing theories and computer programs for either bead models or ellipsoids. Starting from these coefficients, we review the procedures for the calculation of complex solution properties depending on rotational diffusion, such as the decays of electric birefringence and fluorescence anisotropy. We also describe the calculation of the scattering from factor of bead models. The hydrodynamic coefficients and solution properties can be combined to give universal, shape-dependent functions, which were initially intended for ellipsoidal particles, and are extended here for the most general case. We have implemented all three developments in a new computer program. SOLPRO, for calculation of SOLution PROperties, which can be linked to existing software for bead models or ellipsoids.}, Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es}, - Au = {Garcia de la Torre, J and Carrasco, B and Harding, SE}, - Author = {Garcia de la Torre, J and Carrasco, B and Harding, S E}, + Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE}, + Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E}, Da = 19970709, Date-Added = {2008-01-08 15:45:31 -0500}, Date-Modified = {2008-01-08 15:46:57 -0500}, @@ -122,7 +275,8 @@ Pages = {8062-8068}, Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit}, Volume = 119, - Year = 2003} + Year = 2003, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}} @article{Schmidt:2004fj, Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a variety of solutes in a dense fluid of spherical solvent particles. We explore the effects of surface roughness of the solute on the resulting hydrodynamic boundary condition as we naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that when the solute and solvent interact through a purely repulsive isotropic potential, in the Brownian limit the Stokes-Einstein law is satisfied with slip boundary conditions. However, when surface roughness is introduced through an anisotropic solute-solvent interaction potential, we find that the Stokes-Einstein law is satisfied with stick boundary conditions. In addition, when the attractive strength of a short-range isotropic solute-solvent potential is increased, the solute becomes dressed with solvent particles, making it effectively rough, and so stick boundary conditions are again recovered.}, @@ -134,7 +288,8 @@ Pages = {6767-6771}, Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law}, Volume = 108, - Year = 2004} + Year = 2004, + Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}} @article{Klein01, Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein}, @@ -428,7 +583,7 @@ Year = 2003} @article{Cascales98, - Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre}, + Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and {Garc\'{i}a de la Torre}, Jose}, Date-Added = {2008-01-08 14:58:56 -0500}, Date-Modified = {2008-01-08 14:58:57 -0500}, Journal = {J. Phys. Chem. B}, @@ -617,7 +772,9 @@ Title = {{Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers}}, Url = {http://www.biophysj.org/cgi/content/abstract/90/11/L83}, Volume = 90, - Year = 2006} + Year = 2006, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/90/11/L83}, + Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.106.086017}} @article{deJoannis06, Author = {J. de~Joannis and F.~Y. Jiang and J.~T. Kindt}, @@ -773,7 +930,8 @@ Publisher = {American Physical Society}, Title = {Defects in flexible membranes with crystalline order}, Volume = 38, - Year = 1988} + Year = 1988, + Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevA.38.1005}} @article{Monroe95, Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland}, @@ -1095,7 +1253,8 @@ Pages = {2496-2502}, Title = {Electrostatics in periodic slab geometries. I}, Volume = 117, - Year = 2002} + Year = 2002, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}} @article{deJoannis02, Author = {J. {de Joannis} and A. Arnold and C. Holm}, @@ -1108,7 +1267,8 @@ Pages = {2503-2512}, Title = {Electrostatics in periodic slab geometries. II}, Volume = 117, - Year = 2002} + Year = 2002, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.149195}} @article{Barenco95, Author = {A. Barenco and C.~H. Bennett and R. Cleve and D.~P. DiVincenzo and N. Margolus and P. Shor and T. Sleator and J.~A. Smolin and H. Weinfurter}, @@ -1251,7 +1411,8 @@ Pages = {62-67}, Title = {Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry}, Volume = 400, - Year = 2004} + Year = 2004, + Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.cplett.2004.10.086}} @article{Chuang98, Author = {I. Chuang and N. Gershenfeld and M. Kubinec}, @@ -1329,7 +1490,8 @@ Ty = {JOUR}, Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609}, Volume = 88, - Year = 2005} + Year = 2005, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/1/609}} @inbook{Blumen86, Address = {Amsterdam}, @@ -1607,7 +1769,8 @@ Pages = {2213-2216}, Title = {Model for Lamellar Phases of Interacting Lipid Membranes}, Volume = 61, - Year = 1988} + Year = 1988, + Bdsk-File-1 = {YnBsaXN0MDDUAQIDBAUGCQpYJHZlcnNpb25UJHRvcFkkYXJjaGl2ZXJYJG9iamVjdHMSAAGGoNEHCFRyb290gAFfEA9OU0tleWVkQXJjaGl2ZXKoCwwXGBkdJCVVJG51bGzTDQ4PEBEUViRjbGFzc1dOUy5rZXlzWk5TLm9iamVjdHOAB6ISE4ACgAOiFRaABIAGWWFsaWFzRGF0YVxyZWxhdGl2ZVBhdGjSDRobHFdOUy5kYXRhgAVPEQHUAAAAAAHUAAIAAAhnZXplbHRlcgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATkoAAf////8fY2l0LWFicy1lbmRub3RlLTI0I0ZGRkZGRkZGLnJpcwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA/////wAAAAAAAAAAAAAAAAADAAIAABKBY3UAAAAAAAAAAAAAAAAACURvd25sb2FkcwAAAgBILzpob21lOm1hdWw6Z2V6ZWx0ZXI6Z2V6ZWx0ZXI6RG93bmxvYWRzOmNpdC1hYnMtZW5kbm90ZS0yNDIzODAwOC5lbncucmlzAA4AQgAgAGMAaQB0AC0AYQBiAHMALQBlAG4AZABuAG8AdABlAC0AMgA0ADIAMwA4ADAAMAA4AC4AZQBuAHcALgByAGkAcwAPABIACABnAGUAegBlAGwAdABlAHIAEgArL0Rvd25sb2Fkcy9jaXQtYWJzLWVuZG5vdGUtMjQyMzgwMDguZW53LnJpcwAAEwAcL2hvbWUvbWF1bC9nZXplbHRlci9nZXplbHRlcgAJACkAKWNyYm0AAHBvc3gvaG9tZS9tYXVsL2dlemVsdGVyL2dlemVsdGVyAAAAFQACABz//wAA0h4fICFYJGNsYXNzZXNaJGNsYXNzbmFtZaMhIiNdTlNNdXRhYmxlRGF0YVZOU0RhdGFYTlNPYmplY3RfEDMuLi8uLi8uLi9Eb3dubG9hZHMvY2l0LWFicy1lbmRub3RlLTI0MjM4MDA4LmVudy5yaXPSHh8mJ6InI1xOU0RpY3Rpb25hcnkACAARABoAHwApADIANwA6AD8AQQBTAFwAYgBpAHAAeACDAIUAiACKAIwAjwCRAJMAnQCqAK8AtwC5ApEClgKfAqoCrgK8AsMCzAMCAwcDCgAAAAAAAAIBAAAAAAAAACgAAAAAAAAAAAAAAAAAAAMX}} @article{Daw89, Author = {Murray~S. Daw}, @@ -1721,7 +1884,8 @@ Pages = {3668-3675}, Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation}, Volume = 104, - Year = 2000} + Year = 2000, + Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp9937757}} @article{Venable00, Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor}, @@ -1862,7 +2026,8 @@ Pages = {667-683}, Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation}, Volume = 15, - Year = 1994} + Year = 1994, + Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.540150702}} @article{McKinnon92, Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks}, @@ -2589,7 +2754,9 @@ Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}}, Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626}, Volume = 88, - Year = 2005} + Year = 2005, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626}, + Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}} @article{Lenz07, Author = {Olaf Lenz and Friederike Schmid}, @@ -3011,7 +3178,8 @@ Publisher = {American Physical Society}, Title = {Wrinkling transition in partially polymerized vesicles}, Volume = 67, - Year = 1991} + Year = 1991, + Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}} @article{Wendt78, Author = {H. Wendt and F.~F. Abraham}, @@ -3095,7 +3263,8 @@ Ty = {JOUR}, Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}, Volume = 24, - Year = 1969} + Year = 1969, + Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}} @article{Stimson:1926qy, Author = {Stimson, M and Jeffery, GB}, @@ -3136,7 +3305,8 @@ Stat = {PubMed-not-MEDLINE}, Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.}, Volume = 124, - Year = 2006} + Year = 2006, + Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}} @article{sun:031602, Author = {Xiuquan Sun and J. Daniel Gezelter}, @@ -3153,13 +3323,15 @@ Title = {Spontaneous corrugation of dipolar membranes}, Url = {http://link.aps.org/abstract/PRE/v75/e031602}, Volume = 75, - Year = 2007} + Year = 2007, + Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602}, + Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}} @article{Ortega:2007lr, Abstract = {The equivalent radius for any solution property is the radius of a spherical particle having the same value of solution property as that of the macromolecule under consideration. Equivalent radii for different properties present a dependence on size and shape that are more similar than the values of the properties themselves. Furthermore, the ratios of equivalent radii of two properties depend on the conformation (shape or flexibility), but not on the absolute sizes. We define equivalent radii and their ratios, and describe their evaluation for some common models of rigid and flexible macromolecules. Using radii and ratios, we have devised procedures to fit macromolecular models to experimental properties, allowing the determination of the model parameters. Using these quantities, we can construct target functions for an equilibrated, unbiased optimization. The procedures, which have been implemented in public-domain computer programs, are illustrated for rigid, globular proteins, and the rodlike tobacco mosaic virus, and for semiflexible, wormlike heparin molecules.}, Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.}, - Au = {Ortega, A and Garcia de la Torre, J}, - Author = {Ortega, A and Garcia de la Torre, J}, + Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose}, + Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose}, Da = 20070813, Date-Added = {2008-01-08 14:38:03 -0500}, Date-Modified = {2008-01-08 14:38:49 -0500}, @@ -3189,7 +3361,8 @@ Stat = {MEDLINE}, Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.}, Volume = 8, - Year = 2007} + Year = 2007, + Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}} @article{Torre2003, Abstract = {While the prediction of hydrodynamic properties of rigid particles @@ -3215,7 +3388,7 @@ We provide an example of the application of this methodology to the dynamics of a semiflexible, wormlike DNA.}, Annote = {724XK Times Cited:6 Cited References Count:64}, - Author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez}, + Author = {{Garc\'{i}a de la Torre}, Jose and H. E. Sanchez and A. Ortega and J. G. Hernandez and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez}, Issn = {0175-7571}, Journal = {European Biophysics Journal with Biophysics Letters}, Month = {Aug}, @@ -3672,7 +3845,7 @@ Year = 2002} @article{Bernal1980, - Author = {J.M. Bernal and J. G. {de la Torre}}, + Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose}, Journal = {Biopolymers}, Pages = {751-766}, Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape}, @@ -3813,7 +3986,7 @@ them to some test cases, for which the properties are known a priori. We provide guidelines and computational tools for bead modeling.}, Annote = {200TT Times Cited:46 Cited References Count:57}, - Author = {B. Carrasco and J. G. {de la Torre}}, + Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose}, Issn = {0006-3495}, Journal = {Biophysical Journal}, Month = {Jun}, @@ -4234,7 +4407,7 @@ its applicability. Examples include free diffusion, transport in an electric field, and diffusion in a restricting environment.}, Annote = {633AD Times Cited:2 Cited References Count:43}, - Author = {M. X. Fernandes and J. G. {de la Torre}}, + Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose}, Issn = {0006-3495}, Journal = {Biophysical Journal}, Month = {Dec}, @@ -4659,7 +4832,7 @@ Year = 2001} @article{Torre1977, - Author = {Jose Garcia De La Torre, V.A. Bloomfield}, + Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield}, Journal = {Biopolymers}, Pages = {1747-1763}, Title = {Hydrodynamic properties of macromolecular complexes. I. Translation}, @@ -6434,16 +6607,17 @@ Year = 1992} @article{HuseyinKaya07012005, - Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun}, - title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}}, - journal = {Biophys. J.}, - volume = 89, - number = 1, - pages = {520-535}, - doi = {10.1529/biophysj.104.057471}, - year = 2005, - abstract = {It has been demonstrated that a "near-Levinthal" cooperative mechanism, whereby the common G[o] interaction scheme is augmented by an extra favorability for the native state as a whole, can lead to apparent two-state folding/unfolding kinetics over a broad range of native stabilities in lattice models of proteins. Here such a mechanism is shown to be generalizable to a simplified continuum (off-lattice) Langevin dynamics model with a C{alpha} protein chain representation, with the resulting chevron plots exhibiting an extended quasilinear regime reminiscent of that of apparent two-state real proteins. Similarly high degrees of cooperativity are possible in G[o]-like continuum models with rudimentary pairwise desolvation barriers as well. In these models, cooperativity increases with increasing desolvation barrier height, suggesting strongly that two-state-like folding/unfolding kinetics would be achievable when the pairwise desolvation barrier becomes sufficiently high. Besides cooperativity, another generic folding property of interest that has emerged from published experiments on several apparent two-state proteins is that their folding relaxation under constant native stability (isostability) conditions is essentially Arrhenius, entailing high intrinsic enthalpic folding barriers of [~]17-30 kcal/mol. Based on a new analysis of published data on barnase, here we propose that a similar property should also apply to a certain class of non-two-state proteins that fold with chevron rollovers. However, several continuum G[o]-like constructs considered here fail to predict any significant intrinsic enthalpic folding barrier under isostability conditions; thus the physical origin of such barriers in real proteins remains to be elucidated. + Abstract = {It has been demonstrated that a "near-Levinthal" cooperative mechanism, whereby the common G[o] interaction scheme is augmented by an extra favorability for the native state as a whole, can lead to apparent two-state folding/unfolding kinetics over a broad range of native stabilities in lattice models of proteins. Here such a mechanism is shown to be generalizable to a simplified continuum (off-lattice) Langevin dynamics model with a C{alpha} protein chain representation, with the resulting chevron plots exhibiting an extended quasilinear regime reminiscent of that of apparent two-state real proteins. Similarly high degrees of cooperativity are possible in G[o]-like continuum models with rudimentary pairwise desolvation barriers as well. In these models, cooperativity increases with increasing desolvation barrier height, suggesting strongly that two-state-like folding/unfolding kinetics would be achievable when the pairwise desolvation barrier becomes sufficiently high. Besides cooperativity, another generic folding property of interest that has emerged from published experiments on several apparent two-state proteins is that their folding relaxation under constant native stability (isostability) conditions is essentially Arrhenius, entailing high intrinsic enthalpic folding barriers of [~]17-30 kcal/mol. Based on a new analysis of published data on barnase, here we propose that a similar property should also apply to a certain class of non-two-state proteins that fold with chevron rollovers. However, several continuum G[o]-like constructs considered here fail to predict any significant intrinsic enthalpic folding barrier under isostability conditions; thus the physical origin of such barriers in real proteins remains to be elucidated. }, - URL = {http://www.biophysj.org/cgi/content/abstract/89/1/520}, - eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf} -} + Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun}, + Doi = {10.1529/biophysj.104.057471}, + Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf}, + Journal = {Biophys. J.}, + Number = 1, + Pages = {520-535}, + Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}}, + Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520}, + Volume = 89, + Year = 2005, + Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520}, + Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}