DOI: 10.1073/pnas.1334069100. Liquid-solid transition in nuclei of protein crystals

Liquid-solid transition in nuclei of protein crystals

10.1073/pnas.1334069100

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

It is generally assumed that crystallization begins with a small, crystalline nucleus. For proteins this paradigm may not be valid. Our numerical simulations show that under conditions typically used to produce protein crystals, small clusters of model proteins (particles with short-range, attractive interactions) cannot maintain a crystalline structure. Protein crystal nucleation is therefore an indirect, two-step process. A nucleus first forms and grows as a disordered, liquid-like aggregate. Once the aggregate grows beyond a critical size (about a few hundred particles) crystal nucleation becomes possible.

Bibliography

Lomakin, A., Asherie, N., & Benedek, G. B. (2003). Liquid-solid transition in nuclei of protein crystals. Proceedings of the National Academy of Sciences, 100(18), 10254â10257.

Authors 3

Aleksey Lomakin (first)
Neer Asherie (additional)
George B. Benedek (additional)

References 33 Referenced 79

McPherson A. (1999) Crystallization of Biological Macromolecules (Cold Spring Harbor Lab. Press Plainview NY).
10.1073/pnas.101124798
10.1016/S1359-0294(00)00034-0
10.1038/416811a
10.1103/PhysRevLett.76.150
10.1063/1.467526
10.1063/1.466781
10.1103/PhysRevLett.77.4832
10.1103/PhysRevB.51.14899
10.1103/PhysRevE.50.2913
10.1103/PhysRevE.51.1344
10.1103/PhysRevLett.39.474
10.1103/PhysRevE.53.6325
10.1073/pnas.110000497
10.1073/pnas.88.13.5660
10.1063/1.471843
10.1073/pnas.89.4.1214
10.1063/1.474547
10.1016/S0370-1573(97)00021-5
Frenkel D. & Smit D. (1996) Understanding Molecular Simulation: From Algorithms to Applications (Academic San Diego).
Reif F. (1965) Fundamentals of Statistical and Thermal Physics (McGraw-Hill New York).
10.1063/1.470751
Hirschfelder J. O. Curtiss C. F. & Bird R. B. (1954) Molecular Theory of Gases and Liquids (Wiley New York).
Briant, C. L. & Burton, J. J. (1975) Nat. Phys. Sci. 243, 100-102. / Nat. Phys. Sci. (1975)
10.1063/1.431542
10.1103/PhysRevLett.55.226
10.1063/1.467771
Berry R. S. (1999) in Theory of Atomic and Molecular Clusters ed. Jellinek J. (Springer New York) pp. 1-26. (10.1007/978-3-642-58389-6_1)
10.1103/PhysRevLett.86.3570
Wales, D. J., Doye, J. P. K., Miller, M. A., Mortenson, P. N. & Walsh, T. R. (2000) Adv. Chem. Phys. 115, 1-111. / Adv. Chem. Phys. (2000)
10.1073/pnas.96.17.9465
10.1126/science.277.5334.1975
10.1063/1.1446844

Dates

Type	When
Created	21 years, 11 months ago (Sept. 2, 2003, 1:27 p.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 11:15 p.m.)
Indexed	1 month, 3 weeks ago (July 2, 2025, 1:29 p.m.)
Issued	22 years ago (Aug. 18, 2003)
Published	22 years ago (Aug. 18, 2003)
Published Online	22 years ago (Aug. 18, 2003)
Published Print	21 years, 11 months ago (Sept. 2, 2003)

Funders 0

None

BibTeX

@article{Lomakin_2003, title={Liquid-solid transition in nuclei of protein crystals}, volume={100}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.1334069100}, DOI={10.1073/pnas.1334069100}, number={18}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Lomakin, Aleksey and Asherie, Neer and Benedek, George B.}, year={2003}, month=aug, pages={10254–10257} }

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