Periodic Reporting for period 1 - ProFrost (Theoretical and Numerical Analysis of Antifreeze and Ice Nucleator Proteins:Coarse-Grain Approach for Multiscale Study and Bio-Engineering)
Periodo di rendicontazione: 2018-09-01 al 2020-08-31
"In nature life has evolved in order to adapt to a large variety of environmental conditions. In particular, many living beings are capable of surviving in drastic conditions of temperature and pressure, where the water contained in their organism would easily freeze. It is the case, for example, of fishes, insects and plants living in the arctic regions or in desert areas prone to large temperature excursions. Life in such conditions is possible thanks to a special class of ""ice-binding"" proteins that, together with other molecular mechanisms, can control the ice formation in the cells. The ice binding proteins can prevent the growth of ice crystal (anti-freeze proteins) or enhance it (ice-nucleation proteins).
This class of proteins have attracted in recent years the attention of the scientific community given their potential applications in cryo-preservation of tissues and and organs in medicine, storage of frozen foods and lengthening of their shelf life, increasing the freeze tolerance of cultivated plants and farmed fish, production of artificial snow.
The exact mechanisms through which these proteins recognize the ice structure from liquid water and how they bind it are still debated.
The proposed project ProFrost aimed at filling this gap, shedding light on the physical/chemical features that allow these proteins to bind and control the ice. This knowledge can be exploited to design artificial (bio)molecules with properties similar to the ice-binding proteins."
This class of proteins have attracted in recent years the attention of the scientific community given their potential applications in cryo-preservation of tissues and and organs in medicine, storage of frozen foods and lengthening of their shelf life, increasing the freeze tolerance of cultivated plants and farmed fish, production of artificial snow.
The exact mechanisms through which these proteins recognize the ice structure from liquid water and how they bind it are still debated.
The proposed project ProFrost aimed at filling this gap, shedding light on the physical/chemical features that allow these proteins to bind and control the ice. This knowledge can be exploited to design artificial (bio)molecules with properties similar to the ice-binding proteins."
The project focused on a multi-scale approach to characterize the protein-water interplay, with a specific focus on the ice-binding proteins and their capability to control the ice nucleation rate.
We have characterized which are the relevant features that allow an antifreeze-protein (AFP - a special class of ice-binding proteins) to impede the ice-growth. Our results reveal how the AFPs, by pinning the ice surface, force the crystal-liquid interface to bend forming an ice meniscus, causing an increase in the
surface free energy and resulting in a decrease in the freezing point. We have studied how the decrease of the freezing point depends on the average distance between the AFPs (in turn proportional to the concentration of AFPs in the cell). We also have discussed the antifreeze mechanisms in relation to the classical nucleation theory, proposing a theoretical model to describe the observed phenomenon. Finally, we have analyzed how the AFP size, hydropathy and interaction with water affect the capability to control the ice growth.
Aside with this study, our results have provided a further insight in the study of the ice formation in extreme thermodynamic conditions (like negative pressures) and the scaling of the crystal surface tension.
Contemporary we have developed a model-approach to understand how water affect the protein properties. In particular we have described the protein stability and aggregation in water, characterizing the thermal and pressure stability, and the propensity to aggregate according to the protein sequence and the concentration of proteins in solution. This study has allowed to establish a fruitful collaboration with the experimental groups of the CIC biomaGUNE to test our findings.
We have characterized which are the relevant features that allow an antifreeze-protein (AFP - a special class of ice-binding proteins) to impede the ice-growth. Our results reveal how the AFPs, by pinning the ice surface, force the crystal-liquid interface to bend forming an ice meniscus, causing an increase in the
surface free energy and resulting in a decrease in the freezing point. We have studied how the decrease of the freezing point depends on the average distance between the AFPs (in turn proportional to the concentration of AFPs in the cell). We also have discussed the antifreeze mechanisms in relation to the classical nucleation theory, proposing a theoretical model to describe the observed phenomenon. Finally, we have analyzed how the AFP size, hydropathy and interaction with water affect the capability to control the ice growth.
Aside with this study, our results have provided a further insight in the study of the ice formation in extreme thermodynamic conditions (like negative pressures) and the scaling of the crystal surface tension.
Contemporary we have developed a model-approach to understand how water affect the protein properties. In particular we have described the protein stability and aggregation in water, characterizing the thermal and pressure stability, and the propensity to aggregate according to the protein sequence and the concentration of proteins in solution. This study has allowed to establish a fruitful collaboration with the experimental groups of the CIC biomaGUNE to test our findings.
The project has allowed to establish the mutual water-protein interplay, determining the key aspects that, on one side, make a protein capable to control the phase diagram of water (like the ice-binding proteins that alter the melting point of the ice) and on the other side explain how the water hydrogen bonds influence the thermal/pressure/crowding stability of a single protein.
All this results have been exploited to introduce a novel design strategy that will allow to identify new potential sequences, folding in given target structure with certain function, and adapted to specific thermodynamic conditions. Many protein design procedures have been proposed so far, but none accounting explicitly for the properties of the surrounding water. Our approach provide an important step forward, combining water and protein features into a unique design protocol. This last stage of the project is still ongoing and will require further testing.
The importance of developing more accurate schemes to design novel smart material, with applications in medicine and material science is becoming of fundamental importance as the current technology allow to manipulate single molecules and using them as building block to assemble a new generation of materials.
All this results have been exploited to introduce a novel design strategy that will allow to identify new potential sequences, folding in given target structure with certain function, and adapted to specific thermodynamic conditions. Many protein design procedures have been proposed so far, but none accounting explicitly for the properties of the surrounding water. Our approach provide an important step forward, combining water and protein features into a unique design protocol. This last stage of the project is still ongoing and will require further testing.
The importance of developing more accurate schemes to design novel smart material, with applications in medicine and material science is becoming of fundamental importance as the current technology allow to manipulate single molecules and using them as building block to assemble a new generation of materials.