Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol
Abstract
Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2,4-pentanediol (MPD) separately using the R and S enantiomers as well as with a racemic RS mixture. Crystals grown with (R)-MPD had the most order and produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with (R)-MPD and (RS)-MPD the crystal contacts are made by (R)-MPD, demonstrating that there is preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.
- Authors:
-
- Yeshiva Univ., New York, NY (United States); Stanford Univ., Stanford, CA (United States)
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- Yeshiva Univ., New York, NY (United States); Univ. of Pennsylvania, Philadelphia, PA (United States)
- Yeshiva Univ., New York, NY (United States); Yeshiva Univ., Bronx, NY (United States)
- Yeshiva Univ., New York, NY (United States)
- Collegiate School, New York, NY (United States)
- Publication Date:
- Research Org.:
- Brookhaven National Laboratory (BNL), Upton, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1193215
- Report Number(s):
- BNL-108006-2015-JA
Journal ID: ISSN 1399-0047; ABCRE6; R&D Project: LS001
- Grant/Contract Number:
- SC00112704
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Acta Crystallographica. Section D: Biological Crystallography (Online)
- Additional Journal Information:
- Journal Name: Acta Crystallographica. Section D: Biological Crystallography (Online); Journal Volume: 71; Journal Issue: 3; Journal ID: ISSN 1399-0047
- Publisher:
- International Union of Crystallography
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 36 MATERIALS SCIENCE; MPD; crystallization additive; precipitant; high-resolution protein structures; chirality
Citation Formats
Stauber, Mark, Jakoncic, Jean, Berger, Jacob, Karp, Jerome M., Axelbaum, Ariel, Sastow, Dahniel, Buldyrev, Sergey V., Hrnjez, Bruce J., and Asherie, Neer. Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol. United States: N. p., 2015.
Web. doi:10.1107/S1399004714025061.
Stauber, Mark, Jakoncic, Jean, Berger, Jacob, Karp, Jerome M., Axelbaum, Ariel, Sastow, Dahniel, Buldyrev, Sergey V., Hrnjez, Bruce J., & Asherie, Neer. Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol. United States. https://doi.org/10.1107/S1399004714025061
Stauber, Mark, Jakoncic, Jean, Berger, Jacob, Karp, Jerome M., Axelbaum, Ariel, Sastow, Dahniel, Buldyrev, Sergey V., Hrnjez, Bruce J., and Asherie, Neer. Sun .
"Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol". United States. https://doi.org/10.1107/S1399004714025061. https://www.osti.gov/servlets/purl/1193215.
@article{osti_1193215,
title = {Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol},
author = {Stauber, Mark and Jakoncic, Jean and Berger, Jacob and Karp, Jerome M. and Axelbaum, Ariel and Sastow, Dahniel and Buldyrev, Sergey V. and Hrnjez, Bruce J. and Asherie, Neer},
abstractNote = {Chiral control of crystallization has ample precedent in the small-molecule world, but relatively little is known about the role of chirality in protein crystallization. In this study, lysozyme was crystallized in the presence of the chiral additive 2-methyl-2,4-pentanediol (MPD) separately using the R and S enantiomers as well as with a racemic RS mixture. Crystals grown with (R)-MPD had the most order and produced the highest resolution protein structures. This result is consistent with the observation that in the crystals grown with (R)-MPD and (RS)-MPD the crystal contacts are made by (R)-MPD, demonstrating that there is preferential interaction between lysozyme and this enantiomer. These findings suggest that chiral interactions are important in protein crystallization.},
doi = {10.1107/S1399004714025061},
journal = {Acta Crystallographica. Section D: Biological Crystallography (Online)},
number = 3,
volume = 71,
place = {United States},
year = {Sun Mar 01 00:00:00 EST 2015},
month = {Sun Mar 01 00:00:00 EST 2015}
}
Web of Science
Works referenced in this record:
Overview of the CCP 4 suite and current developments
journal, March 2011
- Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods
journal, April 2011
- Gabanyi, Margaret J.; Adams, Paul D.; Arnold, Konstantin
- Journal of Structural and Functional Genomics, Vol. 12, Issue 2
Mechanistic Principles in Chiral Separations Using Liquid Chromatography and Capillary Electrophoresis
journal, April 2006
- Ali, I.; Kumerer, K.; Aboul-Enein, H. Y.
- Chromatographia, Vol. 63, Issue 7-8
New software for searching the Cambridge Structural Database and visualizing crystal structures
journal, May 2002
- Bruno, Ian J.; Cole, Jason C.; Edgington, Paul R.
- Acta Crystallographica Section B Structural Science, Vol. 58, Issue 3
Thermodynamics of the denaturation of lysozyme by guanidine hydrochloride. I. Dependence on pH at 25°
journal, November 1969
- Aune, Kirk C.; Tanford, Charles
- Biochemistry, Vol. 8, Issue 11
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
journal, February 2008
- Hess, Berk; Kutzner, Carsten; van der Spoel, David
- Journal of Chemical Theory and Computation, Vol. 4, Issue 3
Solubility of Thaumatin
journal, June 2008
- Asherie, Neer; Ginsberg, Charles; Blass, Samuel
- Crystal Growth & Design, Vol. 8, Issue 6
Chiral recognition by enantioselective liquid chromatography: Mechanisms and modern chiral stationary phases
journal, February 2010
- Lämmerhofer, Michael
- Journal of Chromatography A, Vol. 1217, Issue 6
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
journal, March 1977
- Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C.
- Journal of Computational Physics, Vol. 23, Issue 3
Isothermal-isobaric molecular dynamics using stochastic velocity rescaling
journal, February 2009
- Bussi, Giovanni; Zykova-Timan, Tatyana; Parrinello, Michele
- The Journal of Chemical Physics, Vol. 130, Issue 7
On vital aid: the why, what and how of validation
journal, January 2009
- Kleywegt, Gerard J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 2
Heterogeneity Determination and Purification of Commercial Hen Egg-White Lysozyme
journal, July 1996
- Thomas, B. R.; Vekilov, P. G.; Rosenberger, F.
- Acta Crystallographica Section D Biological Crystallography, Vol. 52, Issue 4
A Hybrid Mechanism in Chiral Discrimination Induced by Crystallization of Supramolecular Compounds
journal, May 2012
- Amharar, Youness; Grandeury, Arnaud; Sanselme, Morgane
- The Journal of Physical Chemistry B, Vol. 116, Issue 20
Is lysozyme really the ideal model protein?
journal, November 2001
- Chayen, Naomi E.; Saridakis, Emmanuel
- Journal of Crystal Growth, Vol. 232, Issue 1-4
Protein crystallization: from purified protein to diffraction-quality crystal
journal, January 2008
- Chayen, Naomi E.; Saridakis, Emmanuel
- Nature Methods, Vol. 5, Issue 2
Stereoselectivity in the Salt-Cocrystal Products formed by Phenylglycinol or Phenylglycine with their Respective Sodium or Hydrochloride Salts: STEREOSELECTIVITY IN THE SALT-COCRYSTAL PRODUCTS FORMED BY PHENYLGLYCINOL OR PHENYLGLYCINE
journal, September 2012
- Brittain, Harry G.
- Chirality, Vol. 25, Issue 1
PROCHECK: a program to check the stereochemical quality of protein structures
journal, April 1993
- Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.
- Journal of Applied Crystallography, Vol. 26, Issue 2
Tartrate Chirality Determines Thaumatin Crystal Habit
journal, September 2009
- Asherie, Neer; Jakoncic, Jean; Ginsberg, Charles
- Crystal Growth & Design, Vol. 9, Issue 9
Comparative Effects of Salt, Organic, and Polymer Precipitants on Protein Phase Behavior and Implications for Vapor Diffusion
journal, February 2009
- Dumetz, André C.; Chockla, Aaron M.; Kaler, Eric W.
- Crystal Growth & Design, Vol. 9, Issue 2
Resolution of conglomerates by stereoselective habit modifications
journal, March 1982
- Addadi, L.; Berkovitch-Yellin, Z.; Domb, N.
- Nature, Vol. 296, Issue 5852
A Novel Transition-state Analogue for Lysozyme, 4- O -β-Tri- N -acetylchitotriosyl Moranoline, Provided Evidence Supporting the Covalent Glycosyl-enzyme Intermediate
journal, January 2013
- Ogata, Makoto; Umemoto, Naoyuki; Ohnuma, Takayuki
- Journal of Biological Chemistry, Vol. 288, Issue 9
Spontaneous resolution under supramolecular control
journal, January 2002
- Pérez-García, Lluïsa; Amabilino, David B.
- Chem. Soc. Rev., Vol. 31, Issue 6
On the propagation of errors
journal, September 2013
- Jaskolski, Mariusz
- Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 10
Effects of Protein Purity and Precipitant Stereochemistry on the Crystallization of Thaumatin †
journal, December 2008
- Asherie, Neer; Ginsberg, Charles; Greenbaum, Arieh
- Crystal Growth & Design, Vol. 8, Issue 12
Single-wavelength phasing strategy for quasi-racemic protein crystal diffraction data
journal, December 2011
- Sawaya, Michael R.; Pentelute, Brad L.; Kent, Stephen B. H.
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 1
Continuous surface charge polarizable continuum models of solvation. I. General formalism
journal, March 2010
- Scalmani, Giovanni; Frisch, Michael J.
- The Journal of Chemical Physics, Vol. 132, Issue 11
Packing bridges in protein crystal structures
journal, December 2013
- Carugo, Oliviero; Djinović-Carugo, Kristina
- Journal of Applied Crystallography, Vol. 47, Issue 1
Life in the fast lane for protein crystallization and X-ray crystallography
journal, July 2005
- Pusey, M.; Liu, Z.; Tempel, W.
- Progress in Biophysics and Molecular Biology, Vol. 88, Issue 3
High-level theoretical study of the conformational equilibrium of n -pentane
journal, January 2002
- Salam, A.; Deleuze, M. S.
- The Journal of Chemical Physics, Vol. 116, Issue 4
Quantum Mechanical Continuum Solvation Models
journal, August 2005
- Tomasi, Jacopo; Mennucci, Benedetta; Cammi, Roberto
- Chemical Reviews, Vol. 105, Issue 8
The discovery of biological enantioselectivity: Louis Pasteur and the fermentation of tartaric acid, 1857—A review and analysis 150 yr later
journal, January 2007
- Gal, Joseph
- Chirality, Vol. 20, Issue 1
The crystal structure analysis of the relative binding of cisplatin and carboplatin in a mixture with histidine in a protein studied at 100 and 300 K with repeated X-ray irradiation
journal, December 2012
- Helliwell, John R.; Tanley, Simon William Maurice
- Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 1
Cryoprotection properties of salts of organic acids: a case study for a tetragonal crystal of HEW lysozyme
journal, June 2010
- Bujacz, Grzegorz; Wrzesniewska, Blanka; Bujacz, Anna
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 7
Effects of purification on the crystallization of lysozyme
journal, March 1996
- Ewing, Felecia L.; Forsythe, Elizabeth L.; van der Woerd, Mark
- Journal of Crystal Growth, Vol. 160, Issue 3-4
Effect of surface chemistry of novel templates on crystallization of proteins
journal, July 2012
- Tsekova, Daniela S.; Williams, Daryl R.; Heng, Jerry Y. Y.
- Chemical Engineering Science, Vol. 77
The Role of Small Molecule Additives and Chemical Modification in Protein Crystallization
journal, May 2011
- McPherson, A.; Nguyen, C.; Cudney, R.
- Crystal Growth & Design, Vol. 11, Issue 5
Tackling the bottleneck of protein crystallization in the post-genomic era
journal, March 2002
- Chayen, Naomi E.
- Trends in Biotechnology, Vol. 20, Issue 3
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
journal, January 1996
- Jorgensen, William L.; Maxwell, David S.; Tirado-Rives, Julian
- Journal of the American Chemical Society, Vol. 118, Issue 45
Practical Physics Behind Growing Crystals of Biological Macromolecules
journal, May 2012
- Candoni, Nadine; Grossier, Romain; Hammadi, Zoubida
- Protein & Peptide Letters, Vol. 19, Issue 7
Using Graphs to Represent Crystallization Conditions
journal, February 2013
- Chan, Michelle; Fazio, Vincent J.; Newman, Janet
- Crystal Growth & Design, Vol. 13, Issue 3
Efficient Resolution of Enantiomers by Coupling Preferential Crystallization and Dissolution. Part 1: Experimental Proof of Principle
journal, October 2012
- Levilain, Guillaume; Eicke, Matthias J.; Seidel-Morgenstern, Andreas
- Crystal Growth & Design, Vol. 12, Issue 11
Porous silicon: an effective nucleation-inducing material for protein crystallization 1 1Edited by R. Huber
journal, September 2001
- Chayen, N. E.; Saridakis, E.; El-Bahar, R.
- Journal of Molecular Biology, Vol. 312, Issue 4
Structure of tetragonal hen egg-white lysozyme at 0.94 Å from crystals grown by the counter-diffusion method
journal, July 2001
- Sauter, Claude; Otálora, Fermin; Gavira, José-Antonio
- Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 8
The origin of biological homochirality
journal, October 2011
- Blackmond, Donna G.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 366, Issue 1580
Racemic Protein Crystallography
journal, June 2012
- Yeates, Todd O.; Kent, Stephen B. H.
- Annual Review of Biophysics, Vol. 41, Issue 1
Investigation of a Chiral Additive Used in Preferential Crystallization
journal, October 2012
- Gou, Linzhu; Lorenz, Heike; Seidel-Morgenstern, Andreas
- Crystal Growth & Design, Vol. 12, Issue 11
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
The Uppsala Electron-Density Server
journal, November 2004
- Kleywegt, Gerard J.; Harris, Mark R.; Zou, Jin-yu
- Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12
Protecting role of cosolvents in protein denaturation by SDS: a structural study
journal, January 2008
- Michaux, Catherine; Pouyez, Jenny; Wouters, Johan
- BMC Structural Biology, Vol. 8, Issue 1
Crystallization, structure solution and refinement of hen egg-white lysozyme at pH 8.0 in the presence of MPD
journal, August 2000
- Weiss, Manfred S.; Palm, Gottfried J.; Hilgenfeld, Rolf
- Acta Crystallographica Section D Biological Crystallography, Vol. 56, Issue 8
Louis Pasteur, language, and molecular chirality. I. Background and Dissymmetry
journal, December 2010
- Gal, Joseph
- Chirality, Vol. 23, Issue 1
REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011
- Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
Step velocity in tetragonal lysozyme growth as a function of impurity concentration and mass transport conditions
journal, July 2006
- Dold, P.; Ono, E.; Tsukamoto, K.
- Journal of Crystal Growth, Vol. 293, Issue 1
Turning protein crystallisation from an art into a science
journal, October 2004
- Chayen, Naomi E.
- Current Opinion in Structural Biology, Vol. 14, Issue 5
Improved isolation and crystallization of photosystem I for structural analysis
journal, June 1998
- Fromme, Petra; Witt, Horst Tobias
- Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1365, Issue 1-2
The Effect of Temperature and Solution pH on the Nucleation of Tetragonal Lysozyme Crystals
journal, September 1999
- Judge, Russell A.; Jacobs, Randolph S.; Frazier, Tyralynn
- Biophysical Journal, Vol. 77, Issue 3
Pre-assembled clusters distort crystal nucleation kinetics in supersaturated lysozyme solutions
journal, September 2007
- Parmar, Avanish S.; Gottschall, Paul E.; Muschol, Martin
- Biophysical Chemistry, Vol. 129, Issue 2-3
Crystal Growth of Lysozyme Controlled by Laser Trapping
journal, November 2013
- Tu, Jing-Ru; Miura, Atsushi; Yuyama, Ken-ichi
- Crystal Growth & Design, Vol. 14, Issue 1
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
journal, March 1988
- Jorgensen, William L.; Tirado-Rives, Julian
- Journal of the American Chemical Society, Vol. 110, Issue 6
An overview on 2-methyl-2,4-pentanediol in crystallization and in crystals of biological macromolecules
journal, September 2002
- Anand, Kanchan; Pal, Debnath; Hilgenfeld, Rolf
- Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 10
X-ray Structure of Snow Flea Antifreeze Protein Determined by Racemic Crystallization of Synthetic Protein Enantiomers
journal, July 2008
- Pentelute, Brad L.; Gates, Zachary P.; Tereshko, Valentina
- Journal of the American Chemical Society, Vol. 130, Issue 30
Applications of the second virial coefficient: protein crystallization and solubility
journal, April 2014
- Wilson, William W.; DeLucas, Lawrence J.
- Acta Crystallographica Section F Structural Biology Communications, Vol. 70, Issue 5
Efficient Resolution of Enantiomers by Coupling Preferential Crystallization and Dissolution. Part 2: A Parametric Simulation Study to Identify Suitable Process Conditions
journal, March 2013
- Eicke, Matthias J.; Levilain, Guillaume; Seidel-Morgenstern, Andreas
- Crystal Growth & Design, Vol. 13, Issue 4
Controlled Crystallization of Macromolecules using Patterned Substrates in a Sandwiched Plate Geometry
journal, December 2011
- Ghatak, Anindita Sengupta; Ghatak, Animangsu
- Industrial & Engineering Chemistry Research, Vol. 50, Issue 23
The influence of impurities on protein crystallization; the case of lysozyme
journal, March 1993
- Lorber, Bernard; Skouri, Mohammed; Munch, Jean-Pierre
- Journal of Crystal Growth, Vol. 128, Issue 1-4
Molecular replacement with MOLREP
journal, December 2009
- Vagin, Alexei; Teplyakov, Alexei
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
A simple technique for consistently obtaining large single crystals of hen egg-white lysozyme in a concentration gradient of NiCl 2
journal, December 2010
- Magay, Elena; Yoon, Tae-Sung
- Journal of Applied Crystallography, Vol. 44, Issue 1
Shape evolution and thermal stability of lysozyme crystals: effect of pH and temperature
journal, June 2012
- Liang, Miao; Jin, Fengmin; Liu, Rui
- Bioprocess and Biosystems Engineering, Vol. 36, Issue 1
The Cambridge Structural Database: a quarter of a million crystal structures and rising
journal, May 2002
- Allen, Frank H.
- Acta Crystallographica Section B Structural Science, Vol. 58, Issue 3
A smooth particle mesh Ewald method
journal, November 1995
- Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L.
- The Journal of Chemical Physics, Vol. 103, Issue 19
A scheme estimating the energy of intramolecular hydrogen bonds in diols
journal, April 2006
- Mandado, Marcos; Mosquera, Ricardo A.; Alsenoy, Christian Van
- Tetrahedron, Vol. 62, Issue 17
Note on an Approximation Treatment for Many-Electron Systems
journal, October 1934
- Møller, Chr.; Plesset, M. S.
- Physical Review, Vol. 46, Issue 7
A Critical Analysis on the Rotation Barriers in Butane
journal, April 2010
- Mo, Yirong
- The Journal of Organic Chemistry, Vol. 75, Issue 8
Structural studies of the effect that dimethyl sulfoxide (DMSO) has on cisplatin and carboplatin binding to histidine in a protein
journal, April 2012
- Tanley, Simon W. M.; Schreurs, Antoine M. M.; Kroon-Batenburg, Loes M. J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 5
Efficient diffuse function-augmented basis sets for anion calculations. III. The 3-21+G basis set for first-row elements, Li-F
journal, October 1983
- Clark, Timothy; Chandrasekhar, Jayaraman; Spitznagel, G�nther W.
- Journal of Computational Chemistry, Vol. 4, Issue 3
[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997
- Otwinowski, Zbyszek; Minor, Wladek
- Macromolecular Crystallography Part A, 307-326
The Significance of Chirality in Drug Design and Development
journal, April 2011
- H. Brooks, W.; C. Guida, W.; G. Daniel, K.
- Current Topics in Medicinal Chemistry, Vol. 11, Issue 7
Recent progresses in protein-based chiral stationary phases for enantioseparations in liquid chromatography☆
journal, November 2008
- Haginaka, J.
- Journal of Chromatography B, Vol. 875, Issue 1
Processes To Separate Enantiomers
journal, January 2014
- Lorenz, Heike; Seidel-Morgenstern, Andreas
- Angewandte Chemie International Edition, Vol. 53, Issue 5
The effect of protein impurities on lysozyme crystal growth
journal, September 1998
- Judge, Russell A.; Forsythe, Elizabeth L.; Pusey, Marc L.
- Biotechnology and Bioengineering, Vol. 59, Issue 6
Works referencing / citing this record:
An Analysis on Commercial Screening Kits and Chemical Components in Biomacromolecular Crystallization Screening
journal, August 2019
- Qin, Wei; Xie, Si-Xiao; Zhang, Jie
- Crystal Research and Technology, Vol. 54, Issue 9