Research Projects

 

Caterpillar Proteins

Patchy Polymers

Polymers

During my work with Prof Jean-Pierre Hansen, we have shown [1] that the brush profile and height of long grafted polymer chains undergo a rapid transition towards full stretching, thus showing the presence of a rather flat brush/solvent interface.
Our results point to new possibilities in experimental realization of chemically active surfaces, because the height distribution of the end monomer controls the chemical activity of the brush. Moreover the activity of such soft surfaces could be controlled by the length of the grafted polymers. Taking advantage of the experience of Prof Hansen’ s and Dr Barbara Capone on the derivation of effective polymer-polymer interactions, I have recently addressed the problem of constructing the effective interaction potential between self-avoiding polymers grafted on a surface [2].


[1] Coluzza I., Hansen J.P.  Phys. Rev. Lett. 100, 016104 (2008)                   

[2] Coluzza I., Capone B., Hansen J.P.  Soft Matter 7(11),  5255-5259 (2011)

[3] Capone, B., Coluzza, I., LoVerso, F., Likos, C., & Blaak, R. (2012). Physical Review Letters, 109(23), 238301.

 

Virtual Move Parallel Tempering

A major research goal pursued in the group of Prof Frenkel is to develop new simulation techniques. I have contributed to the implementation of a novel Monte Carlo scheme that greatly enhances the power of parallel tempering simulations [1]. In this method, we boost the accumulation of statistical averages by including information about all potential swaps rather than just those swaps that are accepted. As a test, we compute the free-energy landscape for conformational changes in simple model proteins.
With the new technique, the statistical accuracy with which free-energy landscapes are computed, increases by several orders of magnitude.


[1] Coluzza, I. and D. Frenkel. ChemPhysChem, 6, 1779 (2005).

 

Lattice Proteins

Protein Structure Evolution

Allostery


I have conducted a numerical study of the design of protein-like heteropolymers that can refold when the properties of only few monomers are changed [1,2]. The simulations provide a description of a simple allosteric transition by adopting the assumption that the effect of an external agent on a heteropolymer
is to alter the interactions be- tween its constituent monomers. Further, I have characterized the free energy surfaces of the initial and modified protein-like molecules. I have found that there is a region of the conformation space where molecules can be made to refold with minimal free energy cost. Most importantly, this region is accessible by thermal fluctuations. As mentioned above, the efficiency of a motor based on such an allosteric transition would be enhanced by borrowing heat from the environment in the initial stages of the refolding, and by paying it back later. A successful design of the conformational change was achieved for three different substrates and protein sizes. In addition, I have observed that, for free proteins in solution lacking a native conformation, the binding could induce folding to a specific configuration.


Molecular Evolution and Protein Aggregation


One of the key properties of biological molecules is that they can bind strongly to certain substrates, yet interact only weakly with the very large number of other molecules that they encounter in the cellular environment. Using a computationally efficient structural model, I tested several methods to design molecule-substrate binding specificity [3]. I characterized the binding free energy and the binding energy as function of the size of the interacting units. The results of my simulations indicated that there exists a temperature window where specific binding is possible. Binding sites that have been designed to interact strongly with specific substrates are unlikely to bind non-specifically to other substrates. Therefore, the conflict between specific interactions between small numbers of biomolecules, and weak non-specific interaction with the rest, need not be a very serious design constraint.


[1] Coluzza, I., H. G. Muller, and D. Frenkel. Phys. Rev. E., 68, 046703 (2003).

[2] Coluzza, I. and D. Frenkel. Biophysical Journal, 4 (2007).

[3] Coluzza, I. and D. Frenkel. Phys. Rev. E, 70, 051917 (2004).

 

Chaperonin GroEL/GroES

I have been extensively working on the properties of the
GroEL/GroES chaperone system. This protein complex is an example of nature’s masterpieces for molecular machinery. Previously [1] I have shown that an artificial “refolding machine" with structural properties similar to the naturally occurring GroEL/GroES system, could be designed to be able to achieve greater efficiency if a translocation step is included in the reactions cycle. Such a step has not yet been observed experimentally, so in order to support this innovative model we have been exploring the translocation more in detail [2]. Currently I have established a collaboration with the group of Dr Angel Orte and Dr Maria Jose Ruedas at the University of Granada in Spain to conduct experiments on the translocation properties of the equatorial region of the GroEL/GroES complex.



[1] Coluzza, I., S. M. van der Vies, and D. Frenkel, Biophysical Journal, 90, 3375 (2006).

[2] Coluzza, I., A. de Simone, F. Fraternali, and D. Frenkel, PLoS Computational Biology, 4(2), e1000006 (2008).

 
With the Caterpillar protein model I have introduced a novel design procedure that can produce realistic amino acid sequences able to fold into protein structures taken directly from experimental data. In [1-3] I have demonstrated that accurate representation of the protein backbone is a necessary condition for successful protein design, as such constraints confine the possible configurations of proteins to the structural space of real proteins. My hypothesis is based on the observation that the design procedure developed for lattice proteins, when applied to simple off-lattice representations (e.g. a flexible chains of particles), was unable to produce folding sequences.
The key element necessary to reproduce the space of real proteins, is then the definition of a reduced set of constraints that, contrary to Go potentials [4], does not vary from protein to protein. With the caterpillar model I was able to design protein sequences for various proteins representative of the typical combinations of protein secondary structures. Each of the tested sequences reached the target structure with a very high precision considering the simplicity of the model. 
It is important to stress that the three free parameters of the model have been adjusted only on the refolding ability of the designed sequences, and, as a result, the artificial sequences resemble real proteins in the hydrophilic/phobic profiles, and the folding of real sequences predicts the correct native structure with a surprising high accuracy. 

[1] Coluzza I. Plos ONE  6(7), e20853 (2011)
[2]Coluzza, I. (2014). T PloS One, 9(12), e112852. 
[3] Coluzza, I. (2015).  Molecular Physics, (July), 1–8. 
[4] Go, N. and Taketomi, H. P. Natl. Acad. Sci. USA 75(2), 559–563 (1978).Research_files/Coluzza_PlosONE.pdf
The key to the successful development of self-assembled materials
resides in the careful design of the system subunits. Following on the steps outlined by the Caterpillar model, it is possible to define a systematic methodology to construct chains of simple particles, where the linear sequence of particles fully controls the 3D self-assembling of the chain [1,3]. The individual particles forming the chain are spherical decorated with patches that act as interaction sites between them. As for proteins it is possible to design string of particles capable of folding into given target structures. Thus, such colloidal polymers, which could be manufactured in the laboratory with current technology, provide a route to the fabrication of materials with unique non-trivial three dimensional structures.


[1] Coluzza, I., & Dellago, C. (2012). Journal of Physics: Condensed Matter, 24(28), 284111.

[2] Coluzza, I., Van Oostrum, P. D. J., Capone, B., Reimhult, E., & Dellago, C. (2012). Soft Matter.

[3] Coluzza, I., van Oostrum, P., Capone, B., Reimhult, E., & Dellago, C. (2013). Physical Review Letters, 110(7), 075501.


 
A general understanding of the complex phenomenon of protein evolution requires the accurate description of the constraints that define the sub-space of proteins with mutations that do not kill the organism or prevent it from reproducing. Such constraints can have multiple origins, in this work we present a model for constrained evolutionary trajectories represented by a Markovian process throughout
a set of protein-like structures artificially constructed to be topological intermediates between two natural occurring proteins. The number and type of intermediate steps defines how constrained the total evolutionary process is. By using a coarse-grained representation for the protein structures, we derive an analytic formulation of the transition rates between each of the intermediate structures. Knowledge of the transition rates allows for the study of complex evolutionary pathways represented by trajectories through a set of intermediate structures.


[1] Coluzza I., MacDonald J. T., Sadowski M. I., Taylor W. R., Goldstein R. Plos ONE (2012)

 
Research_files/Coluzza_PlosONE_1.pdf
Research_files/Coluzza_Hansen_PhysRevLett.100.016104.pdf
Research_files/Coluzza_Capone_Hansen_SoftMatterc1sm05335c.pdf
Research_files/ChemPhysChem-6_9-1779.pdf
Research_files/PRE46703.pdf
Research_files/Coluzza_Frenkel_BJournal.pdf
Research_files/PRE051917.pdf
Research_files/Coluzza-Vies-Frenkel_BiophJ-90-2006.pdf
Research_files/journal.pcbi.1000006.pdf
http://dx.plos.org/10.1371/journal.pone.0034228

Coupling protein folding/binding: polymer brush

The extent of coupling between the folding of a protein and its bindin
g to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully upon binding. In this Letter, we use Monte Carlo simulations to investigate how disordered polymer chains grafted around a binding site affect the folding and binding of three model proteins. The protein that approaches the substrate fully folded is more hindered during the binding process than those whose folding and binding are cooperative. The polymer chains act as localized crowding agents and can select correctly folded and bound configurations in favor of nonspecifically adsorbed states. The free energy change for forming all intraprotein and protein-substrate contacts can depend nonmonotonically on the polymer length.


[1]  Rubenstein, B., Coluzza, I., & Miller, M.  Physical Review Letters, 108(20), 1-5. (2012)

 
Research_files/PhysRevLett.108.208104.pdf
Research_files/Coluzza,%20Dellago%20-%202012%20-%20The%20configurational%20space%20of%20colloidal%20patchy%20polymers%20with%20heterogeneous%20sequences.pdf
Research_files/Coluzza%20et%20al.%20-%202013%20-%20Design%20and%20folding%20of%20colloidal%20patchy%20polymers.pdf
Research_files/Coluzza%20et%20al.%20-%202013%20-%20Sequence%20controlled%20self-knotting%20colloidal%20patchy%20polymers.pdf
Research_files/Coluzza%20-%202014%20-%20Transferable%20coarse-grained%20potential%20for%20de%20novo%20protein%20folding%20and%20design.pdf
Research_files/Coluzza%20-%202015%20-%20Constrained%20versus%20unconstrained%20folding%20free-energy%20landscapes.pdf