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secondary structures formation is avoided by using short sequence peptides. Derivatization of amino acids is necessary to ease its partition into a C18 bonded phase. Another scale had been developed in 1971 and used peptide retention on hydrophilic gel. 1-butanol and pyridine were used as the mobile phase in this particular scale and glycine was used as the reference value. Pliska and his coworkers used thin layer chromatography to relate mobility values of free amino acids to their hydrophobicities. About a decade ago, another hydrophilicity scale was published, this scale used normal phase liquid chromatography and showed the retention of 121 peptides on an amide-80 column. The absolute values and relative rankings of hydrophobicity determined by chromatographic methods can be affected by a number of parameters. These parameters include the silica surface area and pore diameter, the choice and pH of aqueous buffer, temperature and the bonding density of stationary phase chains.
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of various dielectric medium generated by arrangement of different amino acids. Hence, different parts of the protein structure most likely would behave as solvents with different dielectric values. For simplicity, each protein structure was considered as an immiscible mixture of two solvents, protein interior and protein exterior. The local environment around individual amino acid (termed as "micro-environment") was computed for both protein interior and protein exterior. The ratio gives the relative hydrophobicity scale for individual amino acids. Computation was trained on high resolution protein crystal structures. This quantitative descriptor for microenvironment was derived from the
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tension values for the naturally occurring 20 amino acids in NaCl solution. The main drawbacks of surface tension measurements is that the broken hydrogen bonds and the neutralized charged groups remain at the solution air interface. Another physical property method involve measuring the solvation free energy. The solvation free energy is estimated as a product of an accessibility of an atom to the solvent and an atomic solvation parameter. Results indicate the solvation free energy lowers by an average of 1 Kcal/residue upon folding.
190:
on a bioinformatic survey of 5526 high-resolution structures from the
Protein Data Bank. This differential scale has two comparative advantages: (1) it is especially useful for treating changes in water-protein interactions that are too small to be accessible to conventional force-field calculations, and (2) for homologous structures, it can yield correlations with changes in properties from mutations in the amino acid sequences alone, without determining corresponding structural changes, either in vitro or in vivo.
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making it difficult to obtain pure hydrophobicity scale. Nozaki and
Tanford proposed the first major hydrophobicity scale for nine amino acids. Ethanol and dioxane are used as the organic solvents and the free energy of transfer of each amino acid was calculated. Non liquid phases can also be used with partitioning methods such as micellar phases and vapor phases. Two scales have been developed using micellar phases. Fendler et al. measured the partitioning of 14 radiolabeled amino acids using
141:
tendency for a residue to be found inside of a protein rather than on its surface. Since cysteine forms disulfide bonds that must occur inside a globular structure, cysteine is ranked as the most hydrophobic. The first and third scales are derived from the physiochemical properties of the amino acid side chains. These scales result mainly from inspection of the amino acid structures. Biswas et al., divided the scales based on the method used to obtain the scale into five different categories.
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the increased stability is directly proportional to increase in hydrophobicity up to a certain size limit. The main disadvantage of site-directed mutagenesis method is that not all the 20 naturally occurring amino acids can substitute a single residue in a protein. Moreover, these methods have cost problems and is useful only for measuring protein stability.
158:. Also, amino acid side chain affinity for water was measured using vapor phases. Vapor phases represent the simplest non polar phases, because it has no interaction with the solute. The hydration potential and its correlation to the appearance of amino acids on the surface of proteins was studied by Wolfenden. Aqueous and
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Most of the existing hydrophobicity scales are derived from the properties of amino acids in their free forms or as a part of a short peptide. Bandyopadhyay-Mehler hydrophobicity scale was based on partitioning of amino acids in the context of protein structure. Protein structure is a complex mosaic
228:
methods are based on the measurement of different physical properties. Examples include, partial molar heat capacity, transition temperature and surface tension. Physical methods are easy to use and flexible in terms of solute. The most popular hydrophobicity scale was developed by measuring surface
207:
This method use DNA recombinant technology and it gives an actual measurement of protein stability. In his detailed site-directed mutagenesis studies, Utani and his coworkers substituted 19 amino acids at Trp49 of the tryptophan synthase and he measured the free energy of unfolding. They found that
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for the corresponding types of atoms. A differential solvent accessible surface area hydrophobicity scale based on proteins as compacted networks near a critical point, due to self-organization by evolution, was constructed based on asymptotic power-law (self-similar) behavior. This scale is based
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The most common method of measuring amino acid hydrophobicity is partitioning between two immiscible liquid phases. Different organic solvents are most widely used to mimic the protein interior. However, organic solvents are slightly miscible with water and the characteristics of both phases change
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of a hard-sphere solute with respect to that in the bulk exhibits a linear dependence on cosine value of contact angle. Based on the computed excess chemical potentials of the purely repulsive methane-sized Weeks–Chandler–Andersen solute with respect to that in the bulk, the extrapolated values of
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Palliser and Parry have examined about 100 scales and found that they can use them for locating B-strands on the surface of proteins. Hydrophobicity scales were also used to predict the preservation of the genetic code. Trinquier observed a new order of the bases that better reflect the conserved
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team recently devised a computational approach that can relate the molecular hydrophobicity scale of amino-acid chains to the contact angle of water nanodroplet. The team constructed planar networks composed of unified amino-acid side chains with native structure of the beta-sheet protein. Using
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The
Stephen H. White website provides an example of whole residue hydrophobicity scales showing the free energy of transfer ΔG(kcal/mol) from water to POPC interface and to n-octanol. These two scales are then used together to make Whole residue hydropathy plots. The hydropathy plot constructed
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of the system. In terms of thermodynamics, the hydrophobic effect is the free energy change of water surrounding a solute. A positive free energy change of the surrounding solvent indicates hydrophobicity, whereas a negative free energy change implies hydrophilicity. In this way, the hydrophobic
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The Wimley–White whole residue hydrophobicity scales are significant for two reasons. First, they include the contributions of the peptide bonds as well as the sidechains, providing absolute values. Second, they are based on direct, experimentally determined values for transfer free energies of
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as the most hydrophobic residue, unlike the other two scales. This difference is due to the different methods used to measure hydrophobicity. The method used to obtain the Janin and Rose et al. scales was to examine proteins with known 3-D structures and define the hydrophobic character as the
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phases were used in the development of a novel partitioning scale. Partitioning methods have many drawbacks. First, it is difficult to mimic the protein interior. In addition, the role of self solvation makes using free amino acids very difficult. Moreover, hydrogen bonds that are lost in the
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Reversed phase liquid chromatography (RPLC) is the most important chromatographic method for measuring solute hydrophobicity. The non polar stationary phase mimics biological membranes. Peptide usage has many advantages because partition is not extended by the terminal charges in RPLC. Also,
88:, cannot accept or donate hydrogen bonds to water. Introduction of hexane into water causes disruption of the hydrogen bonding network between water molecules. The hydrogen bonds are partially reconstructed by building a water "cage" around the hexane molecule, similar to that in
667:, (known as Rekker's Fragmental Constants) widely used for pharmacophores. This scale well correlate with the existing methods, based on partitioning and free energy computations. Advantage of this scale is it is more realistic, as it is in the context of real protein structures.
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Zaslavsky, B. Yu.; Mestechkina, N.M.; Miheeva, L.M.; Rogozhin, S.V. (1982). "Measurement of relative hydrophobicity of amino acid side-chains by partition in an aqueous two-phase polymeric system: Hydrophobicity scale for non-polar and ionogenic side-chains".
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shows favorable peaks on the absolute scale that correspond to the known TM helices. Thus, the whole residue hydropathy plots illustrate why transmembrane segments prefer a transmembrane location rather than a surface one.
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character of the genetic code. They believed new ordering of the bases was uracil-guanine-cystosine-adenine (UGCA) better reflected the conserved character of the genetic code compared to the commonly seen ordering UCAG.
1814:
Plass, Monika; Valko, Klara; Abraham, Michael H (1998). "Determination of solute descriptors of tripeptide derivatives based on high-throughput gradient high-performance liquid chromatography retention data".
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Hodges, Robert S.; Zhu, Bing-Yan; Zhou, Nian E.; Mant, Colin T. (1994). "Reversed-phase liquid chromatography as a useful probe of hydrophobic interactions involved in protein folding and protein stability".
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Sharp, Kim A.; Nicholls, Anthony; Friedman, Richard; Honig, Barry (1991-10-08). "Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models".
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Pliška, Vladimir; Schmidt, Manfred; Fauchère, Jean-Luc (1981). "Partition coefficients of amino acids and hydrophobic parameters π of their side-chains as measured by thin-layer chromatography".
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Leodidis, Epaminondas B.; Hatton, T. Alan. (1990). "Amino acids in AOT reversed micelles. 2. The hydrophobic effect and hydrogen bonding as driving forces for interfacial solubilization".
1852:"Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase alpha subunit"
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cosine value of contact angle are calculated(ccHydrophobicity), which can be used to quantify the hydrophobicity of amino acid side chains with complete wetting behaviors.
2157:
Wimley, William C.; Creamer, Trevor P.; White, Stephen H. (1996). "Solvation
Energies of Amino Acid Side Chains and Backbone in a Family of Host−Guest Pentapeptides".
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Palliser, Christopher C.; Parry, David A. D. (2000). "Quantitative comparison of the ability of hydropathy scales to recognize surface ?-strands in proteins".
43:. When consecutively measuring amino acids of a protein, changes in value indicate attraction of specific protein regions towards the hydrophobic region inside
2254:"Characterizing hydrophobicity of amino acid side chains in a protein environment via measuring contact angle of a water nanodroplet on planar peptide network"
1065:
Bandyopadhyay, D., Mehler, E.L. (2008). "Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment".
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A table comparing four different scales for the hydrophobicity of an amino acid residue in a protein with the most hydrophobic amino acids on the top
1108:
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Biswas, Kallol M.; DeVido, Daniel R.; Dorsey, John G. (2003). "Evaluation of methods for measuring amino acid hydrophobicities and interactions".
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One for the transfer of unfolded chains from water to the bilayer interface (referred to as the Wimley–White interfacial hydrophobicity scale).
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molecular dynamics simulation, the team is able to measure the contact angle of water nanodroplet on the planar networks (caHydrophobicity).
680:
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Rose, G.; Geselowitz, A.; Lesser, G.; Lee, R.; Zehfus, M. (1985-08-30). "Hydrophobicity of amino acid residues in globular proteins".
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The hydrophobic or hydrophilic character of a compound or amino acid is its hydropathic character, hydropathicity, or hydropathy.
2032:
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Whole-residue octanol-scale hydropathy plot for the L-subunit of the photosynthetic reaction center of
Rhodobacter sphaeroides.
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The MD simulation system and the structure of artificial beta-folding 2D peptide network composed of unified R-side chains.
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There are clear differences between the four scales shown in the table. Both the second and fourth scales place
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One for the transfer of unfolded chains into octanol, which is relevant to the hydrocarbon core of a bilayer.
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are the amino acids located in that region of the protein. These scales are commonly used to predict the
2252:
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290:Interface scale,
226:physical property
41:membrane proteins
2407:
2353:
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2308:
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113:contributions.
94:solvation shell
62:
56:
12:
11:
5:
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2359:External links
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1127:web.expasy.org
1114:
1073:(2): 646–659.
1054:
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947:(9): 4600–10.
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171:Main article:
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51:
48:
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45:lipid bilayer
42:
38:
34:
30:
26:
22:
18:
2320:
2316:
2306:
2261:
2257:
2247:
2214:
2210:
2204:
2195:
2162:
2159:Biochemistry
2158:
2152:
2111:
2107:
2101:
2090:. Retrieved
2065:
2024:
2020:
2014:
1965:
1961:
1955:
1922:
1918:
1912:
1859:
1855:
1845:
1820:
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1784:
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1418:
1415:Biochemistry
1414:
1408:
1383:
1379:
1373:
1324:
1320:
1314:
1305:
1272:
1269:Biochemistry
1268:
1218:
1214:
1208:
1159:
1155:
1149:
1135:
1126:
1117:
1103:cite journal
1070:
1066:
1024:
1020:
1014:
989:
985:
979:
944:
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324:
317:
305:
293:
268:
257:
253:
244:
223:
206:
197:
176:
148:
135:
128:
71:
49:
16:
15:
1503:Biopolymers
992:: 595–623.
697:engineering
681:nanodroplet
311:(kcal/mol)
299:(kcal/mol)
183:alpha-helix
102:free energy
33:hydrophobic
2395:Biophysics
2389:Categories
2092:2009-06-12
736:References
286:Amino acid
29:amino acid
2231:1056-8700
2179:0006-2960
2128:1545-9993
2041:0887-3585
1990:0028-0836
1939:0003-9861
1886:0027-8424
1837:0021-9673
1801:0021-9673
1766:0020-711X
1723:0021-9673
1679:1539-3755
1628:1539-3755
1577:0022-2836
1523:0006-3525
1479:0021-9673
1435:0006-2960
1400:0022-3654
1349:0022-2844
1289:0006-2960
1243:0036-8075
1184:0028-0836
1041:1056-8700
914:0022-5193
854:0021-9673
765:CiteSeerX
701:dewetting
107:enthalpic
2349:19706896
2298:27803319
2239:10410805
2057:23839522
2049:11119649
2006:21867582
1687:20365015
1636:17358197
1539:25691137
1095:20929779
1087:18247345
971:27442443
862:12877193
724:See also
270:using ΔG
156:micelles
138:cysteine
111:entropic
82:methanol
2340:2741215
2289:5135335
2266:Bibcode
2187:8611495
2144:1823375
2136:8836100
1998:3945310
1970:Bibcode
1947:4839053
1904:3299367
1864:Bibcode
1731:7921179
1659:Bibcode
1608:Bibcode
1531:2331515
1443:1911756
1365:2394979
1357:1206727
1329:Bibcode
1297:7213619
1251:4023714
1223:Bibcode
1215:Science
1200:4338901
1164:Bibcode
1049:8347995
1006:6383201
962:5024328
922:7183857
894:Bibcode
787:7108955
160:polymer
98:entropy
2347:
2337:
2296:
2286:
2237:
2229:
2185:
2177:
2142:
2134:
2126:
2055:
2047:
2039:
2004:
1996:
1988:
1962:Nature
1945:
1937:
1902:
1895:305105
1892:
1884:
1835:
1799:
1764:
1729:
1721:
1685:
1677:
1634:
1626:
1585:994183
1583:
1575:
1537:
1529:
1521:
1477:
1441:
1433:
1398:
1363:
1355:
1347:
1295:
1287:
1249:
1241:
1198:
1192:763335
1190:
1182:
1156:Nature
1093:
1085:
1047:
1039:
1004:
969:
959:
920:
912:
860:
852:
785:
767:
561:−0.07
508:−0.71
505:−0.94
494:−0.02
491:−0.24
463:−0.01
441:−0.06
427:−0.24
424:−2.09
421:−1.85
413:−0.31
399:−0.44
396:−0.67
393:−0.23
385:−0.53
382:−0.46
371:−0.58
368:−1.71
365:−1.13
357:−0.69
354:−1.25
351:−0.56
343:−0.81
340:−1.12
337:−0.31
154:(SDS)
131:Expasy
86:hexane
2140:S2CID
2053:S2CID
2002:S2CID
1535:S2CID
1361:S2CID
1196:S2CID
1091:S2CID
651:2.41
648:3.64
645:1.23
642:Asp-
637:1.81
634:2.80
631:0.99
628:Lys+
623:1.61
620:3.63
617:2.02
614:Glu-
609:1.37
606:2.33
603:0.96
600:His+
595:1.14
592:1.15
589:0.01
581:1.00
578:1.81
575:0.81
572:Arg+
567:0.50
564:0.43
558:Asp0
553:0.43
550:0.85
547:0.42
539:0.33
536:0.46
533:0.13
525:0.33
522:0.50
519:0.17
511:0.23
497:0.22
483:0.19
480:0.77
477:0.58
469:0.12
466:0.11
460:Glu0
455:0.11
452:0.25
449:0.14
438:0.11
435:0.17
432:His0
410:0.14
407:0.45
379:0.07
74:water
2345:PMID
2294:PMID
2235:PMID
2227:ISSN
2183:PMID
2175:ISSN
2132:PMID
2124:ISSN
2045:PMID
2037:ISSN
1994:PMID
1986:ISSN
1943:PMID
1935:ISSN
1900:PMID
1882:ISSN
1833:ISSN
1797:ISSN
1762:ISSN
1727:PMID
1719:ISSN
1683:PMID
1675:ISSN
1632:PMID
1624:ISSN
1581:PMID
1573:ISSN
1527:PMID
1519:ISSN
1475:ISSN
1439:PMID
1431:ISSN
1396:ISSN
1353:PMID
1345:ISSN
1293:PMID
1285:ISSN
1247:PMID
1239:ISSN
1188:PMID
1180:ISSN
1109:link
1083:PMID
1045:PMID
1037:ISSN
1002:PMID
967:PMID
918:PMID
910:ISSN
858:PMID
850:ISSN
838:1000
783:PMID
586:Gly
544:Asn
530:Ser
516:Ala
502:Tyr
488:Cys
474:Gln
446:Thr
418:Trp
404:Pro
390:Met
376:Val
362:Phe
348:Leu
334:Ile
321:woct
309:woct
274:− ΔG
272:woct
109:and
2335:PMC
2325:doi
2321:106
2284:PMC
2274:doi
2262:113
2219:doi
2167:doi
2116:doi
2029:doi
1978:doi
1966:319
1927:doi
1923:161
1890:PMC
1872:doi
1825:doi
1821:803
1789:doi
1785:216
1754:doi
1711:doi
1707:676
1667:doi
1616:doi
1565:doi
1561:105
1511:doi
1467:doi
1463:240
1423:doi
1388:doi
1337:doi
1277:doi
1231:doi
1219:229
1172:doi
1160:277
1075:doi
1029:doi
994:doi
957:PMC
949:doi
902:doi
842:doi
775:doi
761:157
328:wif
323:− Δ
297:wif
276:wif
39:of
27:of
23:or
2391::
2343:.
2333:.
2319:.
2315:.
2292:.
2282:.
2272:.
2260:.
2256:.
2233:.
2225:.
2215:28
2213:.
2181:.
2173:.
2163:35
2161:.
2138:.
2130:.
2122:.
2110:.
2074:^
2051:.
2043:.
2035:.
2025:42
2023:.
2000:.
1992:.
1984:.
1976:.
1964:.
1941:.
1933:.
1921:.
1898:.
1888:.
1880:.
1870:.
1860:84
1858:.
1854:.
1831:.
1819:.
1795:.
1783:.
1760:.
1748:.
1725:.
1717:.
1705:.
1681:.
1673:.
1665:.
1655:80
1653:.
1630:.
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