In recent years, interest in intracellular phases based on proteins and other polymers increases. There is an example of publication here: Hyman, A. A., Weber, C. A., & Jülicher, F. (2014). Liquid-liquid phase separation in biology. Annual review of cell and developmental biology, 30, 39-58 (DOI: 10.1146/annurev-cellbio-100913-013325).
Paradoxically, biophysicists use the word “phase”, but did not say what it means from physical point of view. Understanding the physical nature of the phase is important also because it is linked with such important processes as phase separation, and phase transition.
As to protein, my main question is the following: What are the properties of protein phase differ from properties of trivial protein complex?
My answer. From point of view of physics, phase formation is possible only when main portion of particles of a system changes its physical state in compare with environment. For example, physical state of water molecules in ice is different from the state in liquid water. Basing on this evident physical principle, I believe that protein phase is the phase due to change of physical state of water included in the phase volume because the quantity of water molecules in the phase is much higher (many orders of magnitude) then quantity of protein molecules (mole/mole ratio). Physical state of water in the phase may be changed by binding to proteins only. In contrast, trivial protein complex is filled up by water with the same physical state as bulk water. Phase separation occurs when certain proteins gain the ability to adsorb water. If the protein loses its ability to adsorb water, a phase transition occurs along the following lines: protein-water -----> protein + water.
Who would not agree with me? Please explain why?
http://www.bioparadigma.spb.ru/hidden_history/images/fig44.gif
in my opinion, a phase represent a thermodynamic state of a system which distinguish other systems both theoretically and experimentally. a protein phase represents a potherse within a protein. see my theory: protein thermodynamic structure theory.
I wonder how this discussion might relate to the "microtrabecular structure"-- chiefly protein - proposed by Keith Porter decades ago I'm very interested in this. Thanks.
Dear james:
I beleive that the princiles of protein thermodynamic structure theory is validated for microtrabecular structure of a cell components. the microtrabecular structure of a cell can be divided into many phases or sub-systems in many types. one function of it is related to sub-system of it.
As a first step, I would ask the following question: what is the type of microtrabecular protein(s), globular or natively unfolded? The last type has much more potency to bind water and so to form a phase. Another side of the microtrabecular concept---do we have some protein(s) identified as an element of the microtrabecular structure? Microtrabecular concept is very interesting as unifying protein network ensuring the integrity of the living cell. Thanks James for your conceptual papers infected me by the idea.
Dear Qinyi, your reply is too general to be discussed. We have a relatively simple system: protein dissolved in water. What role do you see for each component in formation of thermodynamic properties of the system?
Dear Matveev:
when protein binds water molecules, its thermodynamic state is changed and many phases can be generated. this can be measured by protein stability, binding ability to other molecules, enzyme activity change, receptor activity change, protein conformational change, local or global, and many other methods of biophysics or biochemistry.
Dear Matveev:
when protein binds water molecules, its thermodynamic state is changed and many phases can be generated. this can be measured by protein stability, binding ability to other molecules, enzyme activity change, receptor activity change, protein conformational change, local or global, and many other methods of biophysics or biochemistry.
Dear Matveev
I am agree with your theory. as you mentioned:
"Basing on this evident physical principle, I believe that protein phase is the phase due to change of physical state of water included in the phase volume because the quantity of water molecules in the phase is much higher"
Anyway, as you know it is not just the "quantity" that maters. water structure at the vicinity of protein and other bio-molecules is different from bulk water. Considering the high concentration of bio-molecules in the cells, actually we can say there is no bulk water! The sol-like structure of water at the cells gives them this chance to define different levels of thermodynamic stability.
As you may have encountered, there are mutated proteins with rather varied structure but they are still functional at cellular level.
Dear Rad,
Thanks for your reply. I am interested in some papers to which I could refer to in order to justify the idea of phase. However, some authors speak about water and are silent about the phase, while others say about the phases, but are silent about water. :(
Dear Vladimir
you may find the following citations useful!
Rohani, Mina, and Gerald H. Pollack. "Flow through horizontal tubes submerged in water in the absence of a pressure gradient: mechanistic considerations." Langmuir 29.22 (2013): 6556-6561.
Pollack, Gerald H. "Comment on “A Theory of Macromolecular Chemotaxis” and “Phenomena Associated with Gel–Water Interfaces. Analyses and Alternatives to the Long-Range Ordered Water Hypothesis”." The Journal of Physical Chemistry B 117.25 (2013): 7843-7846.
Sulbarán, Belkis, et al. "The dynamic development of exclusion zones on cellulosic surfaces." Cellulose 21.3 (2014): 1143-1148.
Pollack, Gerald H. The fourth phase of water: beyond solid, liquid, and vapor. Seattle, 2013.
Thanks Iman. You may find useful the discussion concerning "Comment on “A Theory of Macromolecular Chemotaxis”: http://www.bioparadigma.spb.ru/disc/Pollack-Schurr-Discussion.zip
Do you have some ideas on Prof. Schurr's "Alternatives to the Long-Range Ordered Water Hypothesis..."? It would be interesting to know.
As to me, Prof. Schurr discusses Nafion only. In my presentation (on origin of life), I discuss a wide range of materials in addition to Nafion. Perhaps, Prof. Schurr's alternative explanations are limited by Nafion case.
https://youtu.be/Hn7A-1w0tuQ
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