Abstract
The charge density distribution of a protein has been refined experimentally. Diffraction data for a crambin crystal were measured to ultra-high resolution (0.54 Å) at low temperature by using short-wavelength synchrotron radiation. The crystal structure was refined with a model for charged, nonspherical, multipolar atoms to accurately describe the molecular electron density distribution. The refined parameters agree within 25% with our transferable electron density library derived from accurate single crystal diffraction analyses of several amino acids and small peptides. The resulting electron density maps of redistributed valence electrons (deformation maps) compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide. This study provides validation for experimentally derived parameters and a window into charge density analysis of biological macromolecules.
References
36
Referenced
185
-
P Coppens X-Ray Charge Densities and Chemical Bonding (Oxford Univ. Press, Oxford), pp. 233–286 (1997).
(
10.1093/oso/9780195098235.001.0001
) / X-Ray Charge Densities and Chemical Bonding by Coppens P (1997) -
R F Stewart, B M Craven Biophys J 65, 998–1005 (1993).
(
10.1016/S0006-3495(93)81142-1
) / Biophys J by Stewart R F (1993) -
M A Spackman, P G Byrom Acta Crystallogr B 52, 1023–1035 (1996).
(
10.1107/S0108768196008294
) / Acta Crystallogr B by Spackman M A (1996) -
R W F Bader Atoms in Molecules: A Quantum Theory, eds J Helpern, M L H Green (Oxford Science, Oxford), pp. 288–315 (1990).
(
10.1093/oso/9780198551683.001.0001
) / Atoms in Molecules: A Quantum Theory by Bader R W F (1990) -
M Souhassou, R H Blessing J Appl Crystallogr 32, 210–217 (1999).
(
10.1107/S0021889898011923
) / J Appl Crystallogr by Souhassou M (1999) -
E Espinosa, E Molins, C Lecomte Chem Phys Lett 300, 745–748 (1999).
(
10.1016/S0009-2614(98)01399-2
) / Chem Phys Lett by Espinosa E (1999) -
A D Mesecar, B L Stoddard, D E Koshland Science 277, 202–206 (1997).
(
10.1126/science.277.5323.202
) / Science by Mesecar A D (1997) -
P Coppens Acta Crystallogr A 54, 779–788 (1998).
(
10.1107/S0108767398008575
) / Acta Crystallogr A by Coppens P (1998) -
C Lecomte Advances in Molecular Structure Research, eds I Hargittai, M Hargittai (JAI Press, Greenwich, CT), pp. 261–302 (1995).
(
10.1016/S1087-3295(06)80011-3
) / Advances in Molecular Structure Research by Lecomte C (1995) -
M Souhassou, C Lecomte, N E Ghermani, M M Rohmer, R Wiest, M Bénard, R H Blessing J Am Chem Soc 114, 2371–2382 (1992).
(
10.1021/ja00033a012
) / J Am Chem Soc by Souhassou M (1992) -
F L Hirshfeld Acta Crystallogr A 32, 239–244 (1976).
(
10.1107/S0567739476000533
) / Acta Crystallogr A by Hirshfeld F L (1976) -
V Pichon-Pesme, C Lecomte, H Lachekar J Phys Chem 99, 6242–6250 (1995).
(
10.1021/j100016a071
) / J Phys Chem by Pichon-Pesme V (1995) -
C Jelsch, V Pichon-Pesme, C Lecomte, A Aubry Acta Crystallogr D 54, 1306–1318 (1998).
(
10.1107/S0907444998004466
) / Acta Crystallogr D by Jelsch C (1998) -
C I Bayly, P Cieplak, W D Cornell, P A Kollman J Phys Chem 97, 10269–10280 (1993).
(
10.1021/j100142a004
) / J Phys Chem by Bayly C I (1993) -
U Rao, B Stec, M M Teeter Acta Crystallogr D 51, 914–924 (1995).
(
10.1107/S0907444995002976
) / Acta Crystallogr D by Rao U (1995) -
P G Kraulis J Appl Crystallogr 24, 946–950 (1991).
(
10.1107/S0021889891004399
) / J Appl Crystallogr by Kraulis P G (1991) -
M M Teeter, S M Roe, N H Heo J Mol Biol 230, 292–311 (1993).
(
10.1006/jmbi.1993.1143
) / J Mol Biol by Teeter M M (1993) -
B Stec, R Zhou, M M Teeter Acta Crystallogr D 51, 663–681 (1995).
(
10.1107/S0907444994014484
) / Acta Crystallogr D by Stec B (1995) -
A Yamano, N H Heo, M M Teeter J Biol Chem 272, 9597–9600 (1997).
(
10.1074/jbc.272.15.9597
) / J Biol Chem by Yamano A (1997) -
Z Otwinowski, W Minor Methods Enzymol 276, 307–326 (1997).
(
10.1016/S0076-6879(97)76066-X
) / Methods Enzymol by Otwinowski Z (1997) -
R H Blessing J Appl Crystallogr 30, 421–426 (1997).
(
10.1107/S0021889896014628
) / J Appl Crystallogr by Blessing R H (1997) - R H Blessing, D Y Guo, D A Langs Direct Methods for Solving Macromolecular Structures, NATO ASI Series Volume, Series C: Mathematical and Physical Sciences, ed S Fortier (Kluwer, Dordrecht, The Netherlands) 507, 47–71 (1998). / Direct Methods for Solving Macromolecular Structures, NATO ASI Series Volume, Series C: Mathematical and Physical Sciences by Blessing R H (1998)
-
A T Brünger Nature (London) 355, 472–474 (1992).
(
10.1038/355472a0
) / Nature (London) by Brünger A T (1992) -
N K Hansen, P Coppens Acta Crystallogr A 34, 909–921 (1978).
(
10.1107/S0567739478001886
) / Acta Crystallogr A by Hansen N K (1978) -
G M Sheldrick, T Schneider Methods Enzymol 276, 319–343 (1997).
(
10.1016/S0076-6879(97)77018-6
) / Methods Enzymol by Sheldrick G M (1997) -
F H Allen Acta Crystallogr B 42, 515–522 (1986).
(
10.1107/S0108768186097823
) / Acta Crystallogr B by Allen F H (1986) -
P Coppens, T N Guru Row, P Leung, E D Stevens, P J Becker, Y W Yang Acta Crystallogr A 35, 63–72 (1979).
(
10.1107/S0567739479000127
) / Acta Crystallogr A by Coppens P (1979) -
V S Lamzin, R J Morris, Z Dauter, K S Wilson, M M Teeter J Biol Chem 274, 20753–20755 (1999).
(
10.1074/jbc.274.30.20753
) / J Biol Chem by Lamzin V S (1999) -
A G Urzhumtsev, T P Skovoroda, V Y Lunin J Appl Crystallogr 29, 741–744 (1996).
(
10.1107/S0021889896007194
) / J Appl Crystallogr by Urzhumtsev A G (1996) -
P Coppens Science 158, 1577–1579 (1967).
(
10.1126/science.158.3808.1577
) / Science by Coppens P (1967) -
N Bouhmaida, N-E Ghermani, C Lecomte, A Thalal Acta Crystallogr 53, 556–563 (1998).
(
10.1107/S0108767397004236
) / Acta Crystallogr by Bouhmaida N (1998) -
Z Dauter, V S Lamzin, K S Wilson Curr Opin Struct Biol 7, 681–688 (1997).
(
10.1016/S0959-440X(97)80078-4
) / Curr Opin Struct Biol by Dauter Z (1997) -
S Longhi, M Czjzek, C Cambillau Curr Opin Struct Biol 8, 730–737 (1998).
(
10.1016/S0959-440X(98)80093-6
) / Curr Opin Struct Biol by Longhi S (1998) -
V Lamour, P Barth, H Rogniaux, A Poterszman, E Howard, A Mitschler, A Van Dorsselaer, A Podjarny, D Moras Acta Crystallogr D 55, 721–723 (1999).
(
10.1107/S0907444998013365
) / Acta Crystallogr D by Lamour V (1999) -
C Lecomte, R H Blessing, P Coppens, A Tabard J Am Chem Soc. 108, 6942–6949 (1986).
(
10.1021/ja00282a019
) / J Am Chem Soc. by Lecomte C (1986) - C Lecomte, M M Rohmer, M Bénard in The Porphyrin Handbook: Theoretical and Physical Characterization, eds K M Kadish, K Smith, R Guilard (Academic, New York) 7, 39–79 (1999). / in The Porphyrin Handbook: Theoretical and Physical Characterization by Lecomte C (1999)
Dates
Type | When |
---|---|
Created | 23 years ago (July 26, 2002, 10:41 a.m.) |
Deposited | 1 year, 7 months ago (Jan. 4, 2024, 12:06 a.m.) |
Indexed | 1 month, 3 weeks ago (July 2, 2025, 2:11 p.m.) |
Issued | 25 years, 4 months ago (March 28, 2000) |
Published | 25 years, 4 months ago (March 28, 2000) |
Published Online | 25 years, 4 months ago (March 28, 2000) |
Published Print | 25 years, 4 months ago (March 28, 2000) |
@article{Jelsch_2000, title={Accurate protein crystallography at ultra-high resolution: Valence electron distribution in crambin}, volume={97}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.97.7.3171}, DOI={10.1073/pnas.97.7.3171}, number={7}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Jelsch, Christian and Teeter, Martha M. and Lamzin, Victor and Pichon-Pesme, Virginie and Blessing, Robert H. and Lecomte, Claude}, year={2000}, month=mar, pages={3171–3176} }