| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
2 Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610, USA
Reprint requests to: Valerie Daggett, Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, USA; e-mail: daggett{at}u.washington.edu; fax: (206) 685-3252; or Jane M. Vanderkooi, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059, USA; e-mail: vanderko{at}mail.med.upenn.edu; fax: (215) 573-2042; or William F. DeGrado, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059, USA; e-mail: wdegrado{at}mail.med.upenn.edu; fax: (215) 573-7229.
We examined the hydration of amides of 
3D, a simple, designed three-helix bundle protein. Molecular dynamics calculations show that the amide carbonyls on the surface of the protein tilt away from the helical axis to interact with solvent water, resulting in a lengthening of the hydrogen bonds on this face of the helix. Water molecules are bonded to these carbonyl groups with partial occupancy (
50%–70%), and their interaction geometries show a large variation in their hydrogen bond lengths and angles on the nsec time scale. This heterogeneity is reflected in the carbonyl stretching vibration (amide I' band) of a group of surface Ala residues. The surface-exposed amides are broad, and shift to lower frequency (reflecting strengthening of the hydrogen bonds) as the temperature is decreased. By contrast, the amide I' bands of the buried 13C-labeled Leu residues are significantly sharper and their frequencies are consistent with the formation of strong hydrogen bonds, independent of temperature. The rates of hydrogen-deuterium exchange and the proton NMR chemical shifts of the helical amide groups also depend on environment. The partial occupancy of the hydration sites on the surface of helices suggests that the interaction is relatively weak, on the order of thermal energy at room temperature. One unexpected feature that emerged from the dynamics calculations was that a Thr side chain subtly disrupted the helical geometry 4–7 residues N-terminal in sequence, which was reflected in the proton chemical shifts and the rates of amide proton exchange for several amides that engage in a mixed 310//
-helical conformation.
Keywords: Hydrogen bonding in helices; molecular dynamics; isotope-edited infrared spectroscopy; nuclear magnetic resonance; de novo protein design
Abbreviations: NMR, nuclear magnetic resonance • IR, infrared • 
, chemical shift • HPLC, high performance liquid chromatography • nsec, nanosecond • MD, molecular dynamics
CiteULike 
Connotea 
Del.icio.us 
Digg 
Reddit 
Technorati What's this?
This article has been cited by other articles:
|
|
 |
|
  E. M. Jones, T. C. Squier, and C. A. Sacksteder An Altered Mode of Calcium Coordination in Methionine-Oxidized Calmodulin Biophys. J., December 1, 2008; 95(11): 5268 - 5280. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Kimura, A. Maeda, S. Nishiguchi, K. Ishimori, I. Morishima, T. Konno, Y. Goto, and S. Takahashi Dehydration of main-chain amides in the final folding step of single-chain monellin revealed by time-resolved infrared spectroscopy PNAS, September 9, 2008; 105(36): 13391 - 13396. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Juranic, E. Atanasova, J. H. Streiff, S. Macura, and F. G. Prendergast Solvent-induced differentiation of protein backbone hydrogen bonds in calmodulin Protein Sci., July 1, 2007; 16(7): 1329 - 1337. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Varma and E. Jakobsson The cPLA2 C2{alpha} Domain in Solution: Structure and Dynamics of Its Ca2+-activated and Cation-Free States Biophys. J., February 1, 2007; 92(3): 966 - 976. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-T. Su, S.-H. Kim, and Y.-B. Yan Dissecting the Pretransitional Conformational Changes in Aminoacylase I Thermal Denaturation Biophys. J., January 15, 2007; 92(2): 578 - 587. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Wang, W. L. Lau, W. F. DeGrado, and F. Gai T-Jump Infrared Study of the Folding Mechanism of Coiled-Coil GCN4-p1 Biophys. J., December 1, 2005; 89(6): 4180 - 4187. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. E. Goldberg and A. F. Chaffotte Undistorted structural analysis of soluble proteins by attenuated total reflectance infrared spectroscopy Protein Sci., November 1, 2005; 14(11): 2781 - 2792. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. M. Fesinmeyer, E. S. Peterson, R. B. Dyer, and N. H. Andersen Studies of helix fraying and solvation using 13C' isotopomers Protein Sci., September 1, 2005; 14(9): 2324 - 2332. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Petukhov, G. Rychkov, L. Firsov, and L. Serrano H-bonding in protein hydration revisited Protein Sci., August 1, 2004; 13(8): 2120 - 2129. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Gnanakaran, R. M. Hochstrasser, and A. E. Garcia Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements PNAS, June 22, 2004; 101(25): 9229 - 9234. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhu, D. O. V. Alonso, K. Maki, C.-Y. Huang, S. J. Lahr, V. Daggett, H. Roder, W. F. DeGrado, and F. Gai Ultrafast folding of {alpha}3D: A de novo designed three-helix bundle protein PNAS, December 23, 2003; 100(26): 15486 - 15491. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. W. Wright, G. T. Guffanti, and J. M. Vanderkooi Protein in Sugar Films and in Glycerol/Water as Examined by Infrared Spectroscopy and by the Fluorescence and Phosphorescence of Tryptophan Biophys. J., September 1, 2003; 85(3): 1980 - 1995. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Armen, D. O.V. Alonso, and V. Daggett The role of {alpha}-, 310-, and {pi}-helix in helix->coil transitions Protein Sci., June 1, 2003; 12(6): 1145 - 1157. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
