Direct Link:
1469-896X/asset/olbannerleft.gif?v=1&s=d218899ae53b2862ab119790ed504b8d72122fb3)
1469-896X/asset/olbannerright.gif?v=1&s=59470eb9a1d9b7b13b1be75e9445e6c46ee2214f)
Review
You have full text access to this OnlineOpen article
A review about nothing: Are apolar cavities in proteins really empty?
Article first published online: 12 JAN 2009
DOI: 10.1002/pro.61
Copyright © 2009 The Protein Society
Additional Information
How to Cite
Matthews, B. W. and Liu, L. (2009), A review about nothing: Are apolar cavities in proteins really empty?. Protein Science, 18: 494–502. doi: 10.1002/pro.61
Publication History
- Issue published online: 23 FEB 2009
- Article first published online: 12 JAN 2009
- Accepted manuscript online: 12 JAN 2009 12:00AM EST
- Manuscript Accepted: 24 DEC 2008
- Manuscript Revised: 23 DEC 2008
- Manuscript Received: 11 NOV 2008
Funded by
- NIH. Grant Number: GM21967
References
- 1, , ( 1994) Buried waters and internal cavities in monomeric proteins. Protein Sci 3: 1224–1235.
- 2, , ( 1994) Intramolecular cavities in globular proteins. Protein Eng 7: 613–626.
- 3, ( 1993) Water: now you see it, now you don't. Structure 1: 223–226.
- 4, , , , ( 1995) Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science 267: 1813–1817.
- 5, , , , ( 1995) Use of NMR to detect water within nonpolar protein cavities. Science 270: 1848–1849.
- 6, , ( 1995) Use of NMR to detect water within non-polar cavities. Science 270: 1847–1849.
- 7, , ( 1996) Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities. Biochemistry 35: 4298–4305.
- 8, , , ( 1997) NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules. Nature Struct Biol 4: 396–404.
- 9, ( 1984) Solvation thermodynamics of nonionic solutes. J Chem Phys 81: 2016–2027.
- 10, , , ( 1991) A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins. Biopolymers 31: 919–931.Direct Link:
- 11, , , , ( 1997) Orientational disorder and entropy of water in protein cavities. J Phys Chem B 101: 9380–9389.
- 12, , , ( 1999) Water molecules in the binding cavity of intestinal fatty acid binding protein: dynamic characterization by water 17O and 2H magnetic relaxation dispersion. J Mol Biol 286: 233–246.
- 13, , , ( 2000) Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme. J Mol Biol 302: 955–977.
- 14( 2008) The PyMOL molecular graphics system. Palo Alto, CA, USA: DeLano Scientific LLC. Available at: http://222.pymol.org.
- 15, , , , , ( 2005) Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy. J Am Chem Soc 127: 11676–11683.
- 16, , ( 1986) Internal cavities and buried waters in globular proteins. Biochemistry 25: 3619–3625.
- 17, , , , , ( 1989) Crystal structure of recombinant human interleukin-1β at 2.0Å resolution. J Mol Biol 209: 779–791.
- 18, , ( 1991) High-resolution three-dimensional structure of interleukin 1β in solution by three- and four-dimensional nuclear magnetic resonance spectroscopy. Biochemistry 30: 2315–2323.
- 19, , , ( 1990) Identification and localization of bound internal water in the solution structure of interleukin 1β by heteronuclear three-dimensional proton rotating-fram Overhauser nitrogen-15-proton multiple quantum coherence NMR spectroscopy. Biochemistry 29: 5671–5676.
- 20, , ( 1989) Crystallographic refinement of interleukin 1β at 2.0Å resolution. Proc Natl Acad Sci USA 86: 9667–9671.
- 21, , , , ( 1990) X-ray structural studies of the cytokine interleukin 1β. Prog Clin Biol Res 349: 309–319.
- 22, , , , , , ( 1992) Functional implications of interleukin-1β based on the three-dimensional structure. Proteins 12: 10–23.Direct Link:
- 23, , , , ( 1999) Disordered water within a hydrophobic protein cavity visualized by X-ray crystallography. Proc Natl Acad Sci USA 96: 103–108.
- 24, , ( 2006) Determination of solvent content in cavities in IL-1β using experimentally phased electron density. Proc Natl Acad Sci USA 103: 18148–18153.
- 25, , , ( 1996) Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science 271: 72–77.
- 26, , ( 2008) Use of experimental crystallographic phases to examine the hydration of polar and nonpolar cavities in T4 lysozyme. Proc Natl Acad Sci USA 105: 14406–14411.
- 27, ( 1996) xdlMAPMAN and xdlDATAMAN—programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Cryst D 52: 826–828.Direct Link:
- 28, , , , ( 1997) Contribution of water molecules in the interior of a protein to the conformational stability. J Mol Biol 274: 132–142.
- 29, , , , , , ( 1992) Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 255: 178–183.
- 30, , , , ( 2005) Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proc Natl Acad Sci USA 102: 16668–16671.
- 31, , , , ( 2007) Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography. J Mol Biol 367: 752–763.
- 32, , , , , ( 2001) Filling a cavity dramatically increases pressure stability of the c-Myb R2 subdomain. Proteins 45: 96–101.Direct Link:
- 33, , , , , , , , , ( 1996) The cavity in the hydrophobic core of Myb DNA-binding domain is reserved for DNA recognition and trans-activation. Nature Struct Biol 3: 178–187.
- 34, ( 1994) On the probability of finding a water molecule in a nonpolar cavity. Science 265: 936–937.
- 35, ( 1996) Hydrophilicity of cavities in proteins. Proteins 24: 433–438.Direct Link:
- 36, , , , , , ( 1995) A far infrared study of water diluted in hydrophobic solvents. Mol Phys 84: 769–785.
- 37, , ( 2000) Molecular dynamics of monomeric water dissolved in very hydrophobic solvents: the current state of the art of vibrational spectroscopy analyzed from analytical model and MD simulations. J Phys Chem A 104: 9415–9427.
- 38( 2001) Solvation of a water molecule in cyclohexane and water. Can J Chem 79: 105–109.
- 39, ( 2003) New considerations of the Barclay-Butler rule and the behavior of water dissolved in organic solvents. Biophys Chem 100: 205–220.
- 40( 2005) Solvation thermodynamics of water in nonpolar organic solvents indicate the occurrence of nontraditional hydrogen bonds. J Phys Chem B 109: 981–985.
- 41, , , ( 2003) Formation of water clusters in a hydrophobic solvent. Angew Chem Int Ed 42: 4904–4908.Direct Link:
- 42( 2001) Structural thermodynamics of hydration. J Phys Chem B 105: 12566–12578.
- 43, , , ( 2004) Water clusters in nonpolar cavities. Proc Natl Acad Sci USA 101: 17002–17005.
- 44, ( 2005) Water clusters in a confined nonpolar environment. Chem Phys Lett 410: 348–351.
- 45, ( 2005) Nonpolar solutes enhance water structure within hydration shells while reducing interactions between them. Proc Natl Acad Sci USA 102: 6777–6782.
- 46, , ( 2008) Macroscopically ordered water in nanopores. Proc Natl Acad Sci USA 105: 13218–13222.
- 47, , ( 2008) Water in nonpolar confinement: from nanotubes to proteins and beyond. Ann Rev Phys Chem 59: 713–740.
- 48, , ( 2008) Water clusters confined in nonpolar cavities by ab initio calculations. J Phys Chem C 112: 11779–11785.
- 49, , ( 2006) Solubility of cyclomaltooligosaccharides (cyclodextrins) in H2O and D2O: a comparative study. Carbohydr Res 341: 270–274.
- 50, , Calixarene and related hosts. In: LehnJM, VogtleF, Eds. ( 1996) Comprehensive Supramolecular Chemistry, Vol. 2. Rugby: Pergamon Press, pp 103–142.
- 51, , , , , ( 2004) A bowl-shaped fullerene encapsulates a water into the cage. J Am Chem Soc 126: 2668–2669.
- 52, ( 2004) H2O@open-cage fullerene C60: Control of the encapsulation property and the first mass spectroscopic identification. Tetrahedron Lett 45: 6391–6394.
- 53, , , , , ( 2000) Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer. Nature Struct Biol 7: 772–776.
- 54, , ( 2007) Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion. J Am Chem Soc 129: 7369–7377.