John and Rebecca Moores Professor
Professor of Chemical and Biomolecular Engineering and Chemistry
The primary focus of research in our group is phase transitions that occur in protein solutions.
We are interested in the phase transitions because sometimes proteins in the human cells and tissues form condensed phases—crystals, aggregates, linear polymers, dense liquid droplets, and others—which almost always cause severe debilitating and deadly diseases: sickle cell anemia, eye cataract, Alzheimer’s and other neurological disorders, etc.
Our second set of motives is linked to the fact that the production of medications requires procedures that ensure narrow distributions of the micro-crystallites that comprise the drug preparation—this is a prerequisite for steady drug release. As more and more proteins are being tested for pharmaceutical applications, the need to control the nucleation and growth of protein micro-crystallites will increase.
A third group of factors that underlies our interests in this area is that phase transitions can be used to generate structures inaccessible to other methods—linear arrays of protein molecules, droplets of protein solutions that contain from 1,000 to 10,000 molecules and occupy atto-liter volumes, etc.
Traditionally, the formation of one particular ordered protein phase, the crystal, has been investigated to support the efforts of structural biologists in understanding the atomic structures of the protein molecules, and to shed light on the functions performed by these proteins.
Last but not least, we have argued that protein systems are particularly attractive models to elucidate the general mechanisms of phase transformations. The sizes of the protein molecules, from a few to several tens of nanometers and the characteristic timescales of the processes of growth of the new phases, of a few seconds and longer, are comparable to the lengthscales and time scales accessible to modern analytical techniques. This has allowed in-situ, real-time monitoring of the processes of phase transitions at the molecular scale.
In the logical framework of our research efforts, the first building block is the study of the interactions between the protein molecules in solution. Typically, such investigations are carried out in dilute solutions, relatively far from the phase diagram area of multiple phases, yet they have proven to be useful for a fuller insight into the phase transformations. We use static and dynamic light scattering techniques in house, and, in collaborations with colleagues, small angle x-ray scattering, to determine the second virial coefficient under varying external conditions, and from these data to deduce the potentials of interaction between the molecules. An additional gain from these data is that the second virial coefficient data allow evaluation of the solution non-ideality, and in this way a more accurate definition of the driving forces of the phase transformations.
A second group of efforts aims at determinations of phase diagrams of solutions of different proteins, i.e., on the thermodynamics of phase transformations. Depending on the phase line to be determined, we use microscopy and light scattering techniques.
As far as the kinetics of phase transitions is concerned, we investigate both the kinetics of generation of the new phase via nucleation or spinodal decomposition, and the processes of growth of the new phases.
We have three nucleation projects: we investigate the nucleation of dense liquid droplets of the protein lysozyme and hemoglobin, and its transition into spinodal decomposition as the supersaturation is increased; we investigate the nucleation of the polymer fibers of the sickle cell hemoglobin that underlie the deadly sickle cell anemia, and we investigate the nucleation of protein crystals.
In the area of new phase growth, we investigate the growth processes occurring at molecular, capillary, transport, and macroscopic lengthscales. These include incorporation of molecules into the respective growth sites, generation of growth sites and new layers, in the cases of crystal growth, supply of material to the growth sites by means of solute diffusion, interactions between the growth steps, step bunching and mean to control this phenomenon, defect generation and evolution, etc. We employ scanning probe and interferometry techniques that allow us to cover the various length- and time-scales involved.
- Protein Crystallization
- Physico-chemical aspects of sickle-cell anemia
- Nucleation and phase transitions in protein solutions
- Protein intermolecular interactions and phase diagrams
- Crystallization of membrane proteins
- Kinetics and Stability of Crystal Growth
- 3-D molecular graphics software
- Dr. Oleg Galkin: nucleation and dynamics of formation of protein solid phases
- Weichun Pan: interactions in solutions of proteins
- Yasser Qutub: crystallization of membrane proteins
- Luis Filobelo: nucleation of insulin crystals
- Panagiotis Katsonis: Monte Carlo simulations of phase diagrams
- Dimitra Georgiou: AFM characterization of protein crystals
- Mrinal Shah: pattern formation during phase transitions in protein solutions
April, 2003 — Dr. Vekilov's Research Group
From left: Yasser, Oleg, Panos, Mrinal, Ilya, Olga, Peter, Nick, Dimitra, Luis and Weichun
Byington, M. C., Safari, M. S., Conrad, J. C., & Vekilov, P. G.,
Protein Conformational Flexibility Enables the Formation of Dense Liquid Clusters: Tests Using Solution Shear. Journal of Physical Chemistry Letters, 7(13), 2339-2345 [DOI], 2016
Lu, L., Li, X. J., Vekilov, P. G., & Karniadakis, G. E.,
Probing the Twisted Structure of Sickle Hemoglobin Fibers via Particle Simulations. Biophysical Journal, 110(9), 2085-2093 [DOI], 2016
M.A.C. Potenza, T. Sanvito, F.P. Mariani, P.G. Vekilov, D. Maes.,
Confocal Depolarized Dynamic Light Scattering: a Technique for Complex Fluids. Medical Research Archives, 2(2), 2016
Rittikulsittichai, S., Kolhatkar, A. G., Sarangi, S., Vorontsova, M. A., Vekilov, P. G., Brazdeikis, A., & Lee, T. R.,
Multi-responsive hybrid particles: thermo-, pH-, photo-, and magneto-responsive magnetic hydrogel cores with gold nanorod optical triggers. Nanoscale, 8(23), 11851-11861 [DOI], 2016
Vekilov, P. G.,
Nucleation of protein crystals. Progress in Crystal Growth and Characterization of Materials, 62(2), 136-154 [DOI], 2016
Vekilov, P. G., Chung, S., & Olafson, K. N.,
Shape change in crystallization of biological macromolecules. Mrs Bulletin, 41(5), 375-380 [DOI], 2016
Vorontsova, M. A., Vekilov, P. G., & Maes, D.,
Characterization of the diffusive dynamics of particles with time-dependent asymmetric microscopy intensity profiles. Soft Matter, 12(33), 6926-6936. [DOI], 2016
Li, Y.; Lubchenko, V.; Vekilov, P. G.,
The use of dynamic light scattering and Brownian microscopy to characterize protein aggregation. Review of Scientific Instruments 2011, 82 (5)., 2011
Vekilov, P. G.,
GOLD NANOPARTICLES Grown in a crystal. Nature Nanotechnology 2011, 6 (2), 82-83., 2011
Vekilov, P. G.,
Nucleation of protein condensed phases. Reviews in Chemical Engineering 2011, 27 (1-2), 1-13., 2011
“Kinetics and mechanisms of protein crystallization at the molecular level,” inMethods in Molecular Biology, vol. 300: Protein Nanotechnology, Protocols, Instrumentation, and Applications, edited by T. Vo-Dinh (Humana Press, Totowa, NJ) pp. 15-52, 2005
O. Galkin and P.G. Vekilov,
“Mechanisms of homogeneous nucleation of polymers of sickle cell anemia hemoglobin in deoxy-state,” J. Mol. Biol., 336, 43–59. [Abstract], 2004
“Microscopic, mesoscopic, and macroscopic lengthscales in the kinetics of phase transformations with proteins,” in Nanoscale Structure and Assembly at Solid-fluid Interfaces, edited by J.J. De Yoreo and X.Y. Lui (Kluwer Press, New York) pp. 145-200, 2004
“Dense liquid precursor for the nucleation of ordered solid phases from solution,” Crystal Growth and Design, 4, 671-685, 2004
P.G. Vekilov and O. Galkin,
“Fundamental aspects of nucleation theory revealed in experiments with protein solid phases,” in Nanoscale Structure and Assembly at Solid-fluid Interfaces, edited by X.Y. Lui and J.J. De Yoreo (Kluwer Press, New York) pp. 105-144, 2004
Y. Qutub, I. Reviakine, C. Maxwell, J. Navarro, E. Landau, and P.G. Vekilov,
“Mechanisms of in cubo of growth and defect formation of three-dimensional bacteriorhodopsin crystals,”J. Mol. Biol., 343, 1243-1254, 2004
D.N. Petsev, K. Chen, O. Gliko, and P.G. Vekilov,
“Diffusion-limited kinetics of the solution-solid phase transition of molecular substances,” Proc. Natl. Acad. Sci. USA, 100, 792-796., 2003
I. Reviakine, D.K. Georgiou, P.G. Vekilov,
“Capillarity effects on crystallization kinetics: insulin,” J. Am. Chem. Soc., 125, 11684-11693, 2003
J.J. De Yoreo, P.G. Vekilov,
“Principles of crystal nucleation and growth,” inBiomineralization, edited by P.M. Dove, J.J. De Yoreo, S. Weiner (Mineral Soc. Am., Washington, DC) pp. 57-93, 2003
O. Gliko, I. Reviakine, P.G. Vekilov,
“Stable equidistant step trains during crystallization of insulin,” Phys. Rev. Lett., 90, 225503, 2003
“Molecular mechanisms of defect formation,” in Methods in Enzymology volume 368: Macromolecular Crystallography, Part C, edited by C.W. Carter, Jr., and R.M. Sweet (Academic Press, San Diego) pp. 170-188, 2003
“Solvent entropy effects in the formation of protein solid phases,” in Methods in Enzymology volume 368: Macromolecular Crystallography, Part C, edited by C.W. Carter, Jr., and R.M. Sweet, (Academic Press, San Diego) pp. 84-105, 2003
O. Galkin, K. Chen, R.L. Nagel, R.E. Hirsch, P.G. Vekilov,
“Liquid-liquid separation in solutions of normal and sickle cell hemoglobin,” Proc. Natl. Acad. Sci. USA, 99, 8479-8483 [Abstract], 2002
P.G. Vekilov and A.A. Chernov,
“The Physics of Protein Crystallization,” in Solid State Physics, vol. 57, edited by H. Ehrenreich and F. Spaepen (Academic Press, New York) pp. 1-147, 2002
D.N. Petsev and P.G. Vekilov,
“Evidence for non-DLVO hydration interactions in solutions of the protein apoferritin,” Phys. Rev. Lett., 84, 1339-1342 [Abstract], 2000
O. Galkin and P.G. Vekilov,
“Control of protein crystal nucleation around the metastable liquid-liquid phase boundary,” Proc. Natl. Acad. Sci. USA, 97, 6277-6281 [Abstract], 2000
P.G. Vekilov and J.I.D. Alexander,
“Dynamics of layer growth in protein crystallization,”Chem. Rev., 100, 2061-2089 [Table of Contents], 2000
S.-T. Yau, B.R. Thomas and P.G. Vekilov,
“Molecular mechanisms of crystallization and defect formation,” Phys. Rev. Lett., 85, 353-356 [Abstract], 2000
S.-T. Yau, D.N. Petsev, B.R. Thomas, and P.G. Vekilov,
“Molecular-level thermodynamic and kinetic parameters for the self-assembly of apoferritin molecules into crystals,” J. Mol. Biol., 303, 667-678, 2000