溶媒露出面積

WordNet

on the surface; "surface materials of the moon"
the outer boundary of an artifact or a material layer constituting or resembling such a boundary; "there is a special cleaner for these surfaces"; "the cloth had a pattern of red dots on a white surface"
the outermost level of the land or sea; "earthquakes originate far below the surface"; "three quarters of the Earths surface is covered by water" (同)Earth''s surface
a superficial aspect as opposed to the real nature of something; "it was not what it appeared to be on the surface"
the extended two-dimensional outer boundary of a three-dimensional object; "they skimmed over the surface of the water"; "a brush small enough to clean every dental surface"; "the sun has no distinct surface"
come to the surface (同)come_up, rise up, rise
the extent of a 2-dimensional surface enclosed within a boundary; "the area of a rectangle"; "it was about 500 square feet in area" (同)expanse, surface_area
a part of a structure having some specific characteristic or function; "the spacious cooking area provided plenty of room for servants"
a particular geographical region of indefinite boundary (usually serving some special purpose or distinguished by its people or culture or geography); "it was a mountainous area"; "Bible country" (同)country
a part of an animal that has a special function or is supplied by a given artery or nerve; "in the abdominal region" (同)region
a subject of study; "it was his area of specialization"; "areas of interest include..."
easy to get along with or talk to; friendly; "an accessible and genial man"
capable of being read with comprehension; "readily accessible to the nonprofessional reader"; "the tales seem more approachable than his more difficult novels" (同)approachable
capable of being reached; "a town accessible by rail"
easily obtained; "most students now have computers accessible"; "accessible money"
find the solution to (a problem or question) or understand the meaning of; "did you solve the problem?"; "Work out your problems with the boss"; "this unpleasant situation isnt going to work itself out"; "did you get it?"; "Did you get my meaning?"; "He (同)work_out, figure out, puzzle out, lick, work
capable of meeting financial obligations
a liquid substance capable of dissolving other substances; "the solvent does not change its state in forming a solution" (同)dissolvent, dissolver, dissolving agent, resolvent

PrepTutorEJDIC

(物の)表面,外面;水面 / 《比喩的に》『うわべ』,見かけ / 『表面(水面)の,』表面(水面)に関する / 《比喩的に》『うわべだけの,』見かけだけの / 陸(水)上輸送の / (沈んでいたものが)表面に浮上する;《話》《おどけて》(寝ていた人が)起きる / (…で)…‘に'表面をつける,〈道路〉‘を'舗装する《+名+with+名》
〈U〉〈C〉『面積』 / 〈C〉『地域』,『地方』(region, district) / 〈C〉(活動・研究・興味などの及ぶ)『範囲』,『領域』(range)《+『of』+『名』》 / 〈C〉《英》=areaway 1
(またget-at-able)近づきやすい,入りやすい,達しうる / 《補語にのみ用いて》(感情などに)動かされやすい,(…の)影響を受けやすい《+『to』+『名』》
〈問題など〉‘を'『解く』,解明する,解決する
(借金の)支払い能力がある / 溶解力のある,溶かす / 溶剤,溶媒 / 解決策

Wikipedia preview

出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2013/11/07 18:09:53」(JST)

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Illustration of the solvent accessible surface in comparison to the van der Waals surface. The van der Waals surface as given by the atomic radii is shown in red. The accessible surface is drawn with dashed lines and is created by tracing the center of the probe sphere (in blue) as it rolls along the van der Waals surface. Note that the probe radius depicted here is of smaller scale than the typical 1.4Å.

The accessible surface area (ASA) or solvent-accessible surface area (SASA) is the surface area of a biomolecule that is accessible to a solvent. Measurement of ASA is usually described in units of square ångstroms (a standard unit of measurement in molecular biology). ASA was first described by Lee & Richards in 1971 and is sometimes called the Lee-Richards molecular surface.^[1] ASA is typically calculated using the 'rolling ball' algorithm developed by Shrake & Rupley in 1973.^[2] This algorithm uses a sphere (of solvent) of a particular radius to 'probe' the surface of the molecule.

Methods of calculating ASA[edit]

Shrake-Rupley algorithm[edit]

The Shrake-Rupley algorithm is a numerical method that draws a mesh of points equidistant from each atom of the molecule and uses the number of these points that are solvent accessible to determine the surface area.^[2] The points are drawn at a water molecule's estimated radius beyond the van der Waals radius, which is effectively similar to ‘rolling a ball’ along the surface. All points are checked against the surface of neighboring atoms to determine whether they are buried or accessible. The number of points accessible is multiplied by the portion of surface area each point represents to calculate the ASA. The choice of the 'probe radius' does have an effect on the observed surface area, as using a smaller probe radius detects more surface details and therefore reports a larger surface. A typical value is 1.4Å, which approximates the radius of a water molecule. Another factor that affects the results is the definition of the VDW radii of the atoms in the molecule under study. For example, the molecule may often lack hydrogen atoms which are implicit in the structure. The hydrogen atoms may be implicitly included in the atomic radii of the 'heavy' atoms, with a measure called the 'group radii'. In addition, the number of points created on the van der Waals surface of each atom determines another aspect of discretization, where more points provide an increased level of detail.

LCPO method[edit]

The LCPO method uses a linear approximation of the two-body problem for a quicker analytical calculation of ASA.^[3] The approximations used in LCPO result in an error in the range of 1-3 Å².

Power Diagram method[edit]

Recently a method was presented that calculates ASA fast and analytically using a power diagram.^[4]

Applications[edit]

Accessible surface area is often used when calculating the transfer free energy required to move a biomolecule from aqueous solvent to a non-polar solvent such as a lipid environment. The LCPO method is also used when calculating implicit solvent effects in the molecular dynamics software package AMBER.

It is recently suggested that (predicted) accessible surface area can be used to improve prediction of protein secondary structure.^[5]^[6]

Relation to solvent-excluded surface[edit]

The ASA is closely related to the concept of the solvent-excluded surface (also known as the molecular surface or Connolly surface), which is imagined as a cavity in bulk solvent (effectively the inverse of the solvent-accessible surface). It is also calculated in practice via a rolling-ball algorithm developed by Frederic Richards^[7] and independently implemented three-dimensionally by Michael Connolly in 1983^[8] and Tim Richmond in 1984.^[9] Connolly spent several more years perfecting the method.^[10]

Notes[edit]

^ Lee, B; Richards, FM. (1971). "The interpretation of protein structures: estimation of static accessibility". J Mol Biol 55 (3): 379–400. doi:10.1016/0022-2836(71)90324-X. PMID 5551392.
^ ^a ^b Shrake, A; Rupley, JA. (1973). "Environment and exposure to solvent of protein atoms. Lysozyme and insulin". J Mol Biol 79 (2): 351–71. doi:10.1016/0022-2836(73)90011-9.
^ Weiser J, Shenkin PS, Still WC (1999). "Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)". Journal of Computational Chemistry 20 (2): 217–230. doi:10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A.
^ Klenin K, Tristram F, Strunk T, Wenzel W (2011). "Derivatives of molecular surface area and volume: Simple and exact analytical formulas". Journal of Computational Chemistry 32 (12): 2647–2653.
^ Momen-Roknabadi, A; Sadeghi, M; Pezeshk, H; Marashi, SA (2008). "Impact of residue accessible surface area on the prediction of protein secondary structures". BMC Bioinformatics 9: 357. doi:10.1186/1471-2105-9-357. PMC 2553345. PMID 18759992.
^ Adamczak, R; Porollo, A; Meller, J. (2005). "Combining prediction of secondary structure and solvent accessibility in proteins". Proteins 59 (3): 467–75. doi:10.1002/prot.20441. PMID 15768403.
^ Richards, FM. (1977). "Areas, volumes, packing and protein structure". Annu Rev Biophys Bioeng 6: 151–176. doi:10.1146/annurev.bb.06.060177.001055. PMID 326146.
^ Connolly, M. L. (1983). "Analytical molecular surface calculation". J Appl Cryst 16 (5): 548–558. doi:10.1107/S0021889883010985.
^ Richmond, T. J. (1984). "Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect". J Mol Biol 178 (1): 63–89. doi:10.1016/0022-2836(84)90231-6.
^ Connolly, M. L. (1993). "The molecular surface package". J Mol Graphics 11 (2): 139–141. doi:10.1016/0263-7855(93)87010-3.

References[edit]

Connolly, M. L. (1983). "Solvent-accessible surfaces of proteins and nucleic-acids". Science 221: 709–713. doi:10.1126/science.6879170.
Richmond, Timothy J. (1984). "solvent accessible surface area and excluded volume in proteins". J. Mol. Biol. 178: 63–89. doi:10.1016/0022-2836(84)90231-6.
Connolly, Michael L. (1985). "Computation of molecular volume". J. Amer. Chem. Soc. 107 (5): 118–1124. doi:10.1021/ja00291a006.
Connolly, M. L. (1991). "Molecular interstitial skeleton". Computers and Chemistry 15 (1): 37–45. doi:10.1016/0097-8485(91)80022-E.
Sanner, M.F. (1992). Modelling and Applications of Molecular Surfaces (PhD thesis).
Connolly, M. L. (1992). "Shape distributions of protein topography". Biopolymers 32 (9): 1215–1236. doi:10.1002/bip.360320911.
Blaney, J. M. (1994). Distance Geometry in Molecular Modeling. Rev. Comput. Chem. doi:10.1002/9780470125823.ch6.
Grant, J. A.; Pickup, B. T. (1995). "A Gaussian description of molecular shape". J. Phys. Chem. 99: 3503–3510. doi:10.1021/j100011a016.
Boissonnat, J.-D.; et al. (1994). Computing Connolly Surfaces.
Petitjean, M (1994). "On the Analytical Calculation of van der Waals Surfaces and Volumes: Some Numerical Aspects". J. Comput. Chem. 15 (5). pp. 507–523. doi:10.1002/jcc.540150504.
Connolly, M. L.; et al. (1996). Molecular Surfaces: A Review.
Lin, S. L. (1994). "Molecular surface representations by sparse critical points". Proteins 18: 94–101. doi:10.1002/prot.340180111.
Connolly, M. L.; et al. (2001). Molecular Surfaces: Calculations, Uses and Representations.
Gerstein, M; Richards, F.S. (2001). "Protein geometry: Volumes, areas and distances". CiteSeerX: 10.1.1.134.2539. Missing or empty |url= (help)
Voss, N. R. (2006). "The geometry of the ribosomal polypeptide exit tunnel". J. Mol. Biol. 360 (4): 893–906. doi:10.1016/j.jmb.2006.05.023.
Leach, A. (2001). Molecular Modelling: Principles and Applications (2^nd ed.). p. 7.
Busa, Jan; Dzurina, Jozef; Hayryan, Edik (2005). "ARVO: A fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations". Comp. Phys. Commun. 165: 59–96. doi:10.1016/j.cpc.2004.08.002.

External links[edit]

Network Science, Part 5: Solvent-Accessible Surfaces
AREAIMOL is a command line tool in the CCP4 Program Suite for calculating ASA.
NACCESS solvent accessible area calculations.
Surface Racer Oleg Tsodikov's Surface Racer program. Solvent accessible and molecular surface area and average curvature calculation. Free for academic use.
ASA.py — a Python-based implementation of the Shrake-Rupley algorithm.
Michel Sanner's Molecular Surface – the fastest program to calculate the excluded surface.
pov4grasp render molecular surfaces.
Molecular Surface Package — Michael Connolly's program.
Volume Voxelator — A web-based tool to generate excluded surfaces.
VADAR (Volume, Area, Dihedral Angle Reporter) — A web-based tool for analyzing and assessing peptide and protein structures from their PDB coordinate data.
ASV freeware Analytical calculation of the volume and surface of the union of n spheres (Monte-Carlo calculation also provided).

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