Supramolecular Fuzziness of Intracellular Liquid Droplets: Liquid–Liquid Phase Transitions, Membrane-Less Organelles, and Intrinsic Disorder
Round 1
Reviewer 1 Report
The perspective article on "supramolecular fuzziness of intracellular liquid droplets" covers a very timely subject because our awareness of the variety, composition, formation, functions and importance of these "membrane-less organelles" has been growing rapidly in recent years. The review gives a helpful description of the various types and their locations and a good, clear explanation of our current understanding of their composition, functions, and other properties. I have just a few suggesitons:
Addition of a figure or table would be helpful, perhaps a table of examples, their cellular locations, and functions
The section containing lines 58-67 about factors affecting formation would be better after the paragraphs about the specific types, so after line 102.
remove "the" in line 15, line 15 again, 19, 57, 59, 156, 2 places in 186, 2 places in 187, before differently in 188, 199, 251, 253
line 56 - a membrane
62 - a multitude
69 -considered to be
74 the nucleus contains
76 remove 2nd of?, and remove the before Sam 68
84 compositions
87 distributions
105 lack of surrounding membranes
128 Because the components of a dense core are brought together at the early states of the SG assembly, whereas a diffuse shell of these PMLOs is formed
143 well suited
144 responses
151 the majority
190 unique position in the
193 interactions
205 high sensitivity and
206 because of this
208 in the regulation
233 in the spindle
239 conformational diversity
249 retain a highly mobile
253 In summary,
255 when undergoing
Author Response
The perspective article on "supramolecular fuzziness of intracellular liquid droplets" covers a very timely subject because our awareness of the variety, composition, formation, functions and importance of these "membrane-less organelles" has been growing rapidly in recent years. The review gives a helpful description of the various types and their locations and a good, clear explanation of our current understanding of their composition, functions, and other properties.
REPLY: Thank you for careful reading of the manuscript, helpful suggestions and high evaluation of this work.
I have just a few suggestions:
Addition of a figure or table would be helpful, perhaps a table of examples, their cellular locations, and functions
REPLY: To address this suggestion, a figure was added showing LLPT and factors triggering this transition.
The section containing lines 58-67 about factors affecting formation would be better after the paragraphs about the specific types, so after line 102.
REPLY: Corrected
remove "the" in line 15, line 15 again, 19, 57, 59, 156, 2 places in 186, 2 places in 187, before differently in 188, 199, 251, 253
REPLY: Corrected
line 56 - a membrane
REPLY: Corrected
62 - a multitude
REPLY: Corrected
69 -considered to be
REPLY: Corrected
74 the nucleus contains
REPLY: Corrected
76 remove 2nd of?, and remove the before Sam 68
REPLY: Corrected
84 compositions
REPLY: Corrected
87 distributions
REPLY: Corrected
105 lack of surrounding membranes
REPLY: Corrected
128 Because the components of a dense core are brought together at the early states of the SG assembly, whereas a diffuse shell of these PMLOs is formed
REPLY: Corrected
143 well suited
REPLY: Corrected
144 responses
REPLY: Corrected
151 the majority
REPLY: Corrected
190 unique position in the
REPLY: Corrected
193 interactions
REPLY: Corrected
205 high sensitivity and
REPLY: Corrected
206 because of this
REPLY: Corrected
208 in the regulation
REPLY: Corrected
233 in the spindle
REPLY: Corrected
239 conformational diversity
REPLY: Corrected
249 retain a highly mobile
REPLY: Corrected
253 In summary,
REPLY: Corrected
255 when undergoing
REPLY: Corrected
Reviewer 2 Report
The article is well written, treat an interesting issue, reads well and is logically sound. Since the manuscript type is perspective, physical chemistry section some questions should be addressed to improve the potential readers.
Chapter 1, row 53 to 63: the author discusses “LLPTs causing the PMLO formation may be triggered by a variety of environmental factors”. At the end of this discussion, the author should introduce the physical chemistry of this behavior i.e. Chemical equilibrium between aggregate and monomeric molecules that is the basis of PMLO formation and how changes in thermodynamic coordinate change the equilibrium.
Chapter 1, row 109: “…and possess sufficient surface tension for maintenance of their spherical shape.” Discuss the calculation of Gibbs free energy of PMLO since surface tension multiplied to SASA has done delta G and not only to the morphology.
Chapter 2. In this paragraph, IDSs behavior is discussed. Any discussion about amyloidogenic proteins is done. This class of proteins covers a very important field of IDPs since many pathologies are involved (see type II diabetes, Parkinson and Alzheimer diseases). Moreover, the physical chemistry of amyloidogenic proteins has contributed to increasing our knowledge about the structure and dynamics of amyloid and amyloidogenic proteins. Amyloidogenic proteins form soluble unstructured transient aggregates that are responsible for the toxicity of some IDPs such as human IAPP, beta-amyloid, and alpha-synuclein. The LLPTs approach could give a new impulse to understanding the molecular mechanisms of their toxicity. Besides, it has recently been reported that IDPs form stable aggregates in the liquid phase even with free phospholipids in solution (10.1063/1.4948323; 10.1021/acs.jpclett.8b02241).
Last research can be find on the following papers: doi:10.1021/ja900285z; 10.1021/jp511758w; 10.1038/srep28658; 10.1021/ja405993r; 10.1021/acschemneuro.7b00110.
Last, please discuss G-quadruplexes another interesting class of PLMOs molecules (some information can be found on DOI: 10.1016/j.bmc.2013.12.051; 10.1016/j.tibtech.2017.06.012)
Author Response
The article is well written, treat an interesting issue, reads well and is logically sound. Since the manuscript type is perspective, physical chemistry section some questions should be addressed to improve the potential readers.
REPLY: Thank you for careful reading of the manuscript, helpful suggestions and high evaluation of this work.
Chapter 1, row 53 to 63: the author discusses “LLPTs causing the PMLO formation may be triggered by a variety of environmental factors”. At the end of this discussion, the author should introduce the physical chemistry of this behavior i.e. Chemical equilibrium between aggregate and monomeric molecules that is the basis of PMLO formation and how changes in thermodynamic coordinate change the equilibrium.
REPLY: To address this issue, a figure was added showing LLPT and factors triggering this transition.
Chapter 1, row 109: “…and possess sufficient surface tension for maintenance of their spherical shape.” Discuss the calculation of Gibbs free energy of PMLO since surface tension multiplied to SASA has done delta G and not only to the morphology.
REPLY: I am not sure that addition of this discussion is needed. In my view, this discussion is unrelated to the subject of this perspective.
Chapter 2. In this paragraph, IDSs behavior is discussed. Any discussion about amyloidogenic proteins is done. This class of proteins covers a very important field of IDPs since many pathologies are involved (see type II diabetes, Parkinson and Alzheimer diseases). Moreover, the physical chemistry of amyloidogenic proteins has contributed to increasing our knowledge about the structure and dynamics of amyloid and amyloidogenic proteins. Amyloidogenic proteins form soluble unstructured transient aggregates that are responsible for the toxicity of some IDPs such as human IAPP, beta-amyloid, and alpha-synuclein. The LLPTs approach could give a new impulse to understanding the molecular mechanisms of their toxicity.
REPLY: Although formation of oligomers by amyloidogenic IDPs is not related to the subject of this article, discussion of the “aging” of PMLOs, their pathological transformation and potential relation of these processes to the pathogenesis of human diseases was added to the revised manuscript as a new section entitled “Dysregulation of the biogenesis of intracellular liquid droplets and disease”.
Besides, it has recently been reported that IDPs form stable aggregates in the liquid phase even with free phospholipids in solution (10.1063/1.4948323; 10.1021/acs.jpclett.8b02241). Last research can be find on the following papers: doi:10.1021/ja900285z; 10.1021/jp511758w; 10.1038/srep28658; 10.1021/ja405993r; 10.1021/acschemneuro.7b00110.
REPLY: Although these observations are interesting, they are not related to PMLOs and therefore their discussion is not included to the manuscript.
Last, please discuss another interesting class of PLMOs molecules (some information can be found on DOI: 10.1016/j.bmc.2013.12.051; 10.1016/j.tibtech.2017.06.012)
REPLY: Although the mentioned papers describe structure and various applications of G-quadruplexes, they do not discuss G-quadruplexes as “another interesting class of PLMOs molecules”. There is not a single paper in PubMed that would discuss “G-quadruplex and liquid-liquid phase transition” or “G-quadruplex and liquid-liquid phase separation”, or “G-quadruplex membrane-less organelle”. Therefore, the proposed subject is unrelated to the topic of this perspective article.
Round 2
Reviewer 2 Report
The author has not satisfied any of the questions I have raised. Perhaps I was not clear enough. I would like to remind the author that this manuscript is a perspective and will be published in the Chemical-physical section. I have suggested some references that address the problem from Physical-Chemistry. In fact, the bibliography reported in the manuscript does not contain even one article pertinent to the Physical-Chemistry.
Polyamorphism is the capability of a material to exist in a different amorphous state. Many amorphous substances can exist in the different amorphous state (e.g. polymers, water, silica and so on). Polyamorphism requires two distinct amorphous states with a clear and discontinuous (Volume, Enthalpy, and Entropy) first-order phase transition. If a transition occurs between two stable liquid states, we will define a liquid-liquid phase transition.
All my suggestions are included in this liquid-liquid phase transitions.
Being the manuscript a perspective, the reader expects to find also suggestions of systems not currently studied in this view, but showing the characteristics treated in the manuscript (see G-Quadruplex).
REPLY1: I am not sure that the addition of this discussion is needed. In my view, this discussion is unrelated to the subject of this perspective.
Thermodynamics and chemical-equilibrium is the basic argument to treat any phase transition, please improve this topic.
REPLY2: Although formation of oligomers by amyloidogenic IDPs is not related to the subject of this article, discussion of the “aging” of PMLOs, their pathological transformation and potential relation of these processes to the pathogenesis of human diseases was added to the revised manuscript as a new section entitled “Dysregulation of the biogenesis of intracellular liquid droplets and disease”.
Not agree, in fact, the author discusses some question about apha-synuclein, an IDP. Are IAPP and Abeta IDP or not.
REPLY: Although these observations are interesting, they are not related to PMLOs and therefore their discussion is not included in the manuscript.
Not agree at all. See you my previous reply.
REPLY: Although the mentioned papers describe the structure and various applications of G-quadruplexes, they do not discuss G-quadruplexes as “another interesting class of PLMOs molecules”. There is not a single paper in PubMed that would discuss “G-quadruplex and liquid-liquid phase transition” or “G-quadruplex and liquid-liquid phase separation”, or “G-quadruplex membrane-less organelle”. Therefore, the proposed subject is unrelated to the topic of this perspective article.
I discuss this point in the first paragraph of this letter.
