Macromolecular crowding: Macromolecules friend or foe.

BACKGROUND Cellular interior is known to be densely crowded due to the presence of soluble and insoluble macromolecules, which altogether occupy ~40% of the total cellular volume. This results in altered biological properties of macromolecules. SCOPE OF REVIEW Macromolecular crowding is observed to have both positive and negative effects on protein folding, structure, stability and function. Significant data has been accumulated so far on both the aspects. However, most of the review articles so far have focused on the positive aspect of macromolecular crowding and not much attention has been paid on the deleterious aspect of crowding on macromolecules. In order to have a complete knowledge of the effect of macromolecular crowding on proteins and enzymes, it is important to look into both the aspects of crowding to determine its precise role under physiological conditions. To fill the gap in the understanding of the effect of macromolecular crowding on proteins and enzymes, this review article focuses on the deleterious influence of crowding on macromolecules. MAJOR CONCLUSIONS Macromolecular crowding is not always good but also has several deleterious effects on various macromolecular properties. Taken together, the properties of biological macromolecules in vivo appears to be finely regulated by the nature and level of the intracellular crowdedness in order to perform their biological functions appropriately. GENERAL SIGNIFICANCE The information provided here gives an understanding of the role played by the nature and level of cellular crowdedness in intensifying and/or alleviating the burden of various proteopathies.

[1]  J. M. Sanchez-Ruiz,et al.  Lower kinetic limit to protein thermal stability: A proposal regarding protein stability in vivo and its relation with misfolding diseases , 2000, Proteins.

[2]  I. Pozdnyakova,et al.  Non-linear effects of macromolecular crowding on enzymatic activity of multi-copper oxidase. , 2010, Biochimica et biophysica acta.

[3]  A. Minton,et al.  Macromolecular Crowding Accelerates Amyloid Formation by Human Apolipoprotein C-II* , 2002, The Journal of Biological Chemistry.

[4]  Gengfu Xiao,et al.  Macromolecular crowding converts the human recombinant PrPc to the soluble neurotoxic β‐oligomers , 2010, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[5]  J. Herzfeld,et al.  Macromolecular diffusion in crowded solutions. , 1993, Biophysical journal.

[6]  Zoya Ignatova,et al.  Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Yves F. Dufrêne,et al.  Calcium Ions Promote Formation of Amyloid β-Peptide (1–40) Oligomers Causally Implicated in Neuronal Toxicity of Alzheimer's Disease , 2011, PloS one.

[8]  A. Minton,et al.  Evidence for protein self-association induced by excluded volume. Myoglobin in the presence of globular proteins. , 1981, Biochimica et biophysica acta.

[9]  R. Swaminathan,et al.  Effect of crowding by dextrans and Ficolls on the rate of alkaline phosphatase-catalyzed hydrolysis: a size-dependent investigation. , 2006, Biopolymers.

[10]  Huan-Xiang Zhou,et al.  Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins. , 2004, Accounts of chemical research.

[11]  Joost Schymkowitz,et al.  Gain of function of mutant p53 by coaggregation with multiple tumor suppressors. , 2011, Nature chemical biology.

[12]  N. Sugimoto,et al.  Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions. , 2009, Journal of the American Chemical Society.

[13]  B. Derham,et al.  The effect of the presence of globular proteins and elongated polymers on enzyme activity. , 2006, Biochimica et biophysica acta.

[14]  Zhengguo Zhou,et al.  Crowded Cell-like Environment Accelerates the Nucleation Step of Amyloidogenic Protein Misfolding* , 2009, The Journal of Biological Chemistry.

[15]  G. Careri,et al.  Protein hydration and function. , 1991, Advances in protein chemistry.

[16]  Jun-Mo Yang,et al.  Effects of macromolecular crowding on refolding of recombinant human brain-type creatine kinase. , 2012, International journal of biological macromolecules.

[17]  R. Chowhan,et al.  POLYAMINES IN MODULATING PROTEIN AGGREGATION , 2013 .

[18]  K. Weber,et al.  Microtubule formation by pure brain tubulin in vitro. The influence of dextran and poly(ethylene glycol). , 1978, European journal of biochemistry.

[19]  S. Zimmerman,et al.  Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. , 1991, Journal of molecular biology.

[20]  Dirar Homouz,et al.  Crowded, cell-like environment induces shape changes in aspherical protein , 2008, Proceedings of the National Academy of Sciences.

[21]  Heather A. O'Neill,et al.  Small heat shock proteins and α-crystallins: dynamic proteins with flexible functions. , 2012, Trends in biochemical sciences.

[22]  Wei Li,et al.  Macromolecular crowding modulates the kinetics and morphology of amyloid self-assembly by β-lactoglobulin. , 2013, International journal of biological macromolecules.

[23]  P. Stewart,et al.  Structure and mechanism of protein stability sensors: chaperone activity of small heat shock proteins. , 2009, Biochemistry.

[24]  P. Lansbury,et al.  Molecular crowding accelerates fibrillization of alpha-synuclein: could an increase in the cytoplasmic protein concentration induce Parkinson's disease? , 2002, Biochemistry.

[25]  Huan‐Xiang Zhou,et al.  Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. , 2008, Annual review of biophysics.

[26]  F. Ahmad,et al.  Forty years of research on osmolyte-induced protein folding and stability , 2011 .

[27]  M. Cascante,et al.  Effect of crowding by dextrans on the hydrolysis of N-Succinyl-L-phenyl-Ala-p-nitroanilide catalyzed by α-chymotrypsin. , 2011, The journal of physical chemistry. B.

[28]  Zhengguo Zhou,et al.  Mixed Macromolecular Crowding Accelerates the Oxidative Refolding of Reduced, Denatured Lysozyme , 2004, Journal of Biological Chemistry.

[29]  A. Minton,et al.  Tracer diffusion of globular proteins in concentrated protein solutions. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Gary J. Pielak,et al.  Impact of reconstituted cytosol on protein stability , 2013, Proceedings of the National Academy of Sciences.

[31]  T. Laurent.  THE INTERACTION BETWEEN POLYSACCHARIDES AND OTHER MACROMOLECULES. 5. THE SOLUBILITY OF PROTEINS IN THE PRESENCE OF DEXTRAN. , 1963, The Biochemical journal.

[32]  Jun-Mo Yang,et al.  Inactivation of Recombinant Human Brain-Type Creatine Kinase During Denaturation by Guanidine Hydrochloride in a Macromolecular Crowding System , 2012, Applied Biochemistry and Biotechnology.

[33]  D S Goodsell,et al.  Inside a living cell. , 1991, Trends in biochemical sciences.

[34]  A. Muga,et al.  Excluded Volume Effects on the Refolding and Assembly of an Oligomeric Protein , 2001, The Journal of Biological Chemistry.

[35]  Dirar Homouz,et al.  Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding , 2010, Proceedings of the National Academy of Sciences.

[36]  Zhengguo Zhou,et al.  Mixed macromolecular crowding accelerates the refolding of rabbit muscle creatine kinase: implications for protein folding in physiological environments. , 2006, Journal of molecular biology.

[37]  A. Minton.  Implications of macromolecular crowding for protein assembly. , 2000, Current opinion in structural biology.

[38]  T. Laurent.  Enzyme reactions in polymer media. , 1971, European journal of biochemistry.

[39]  Zhihong Guo,et al.  Effects of Macromolecular Crowding on the Intrinsic Catalytic Efficiency and Structure of Enterobactin-Specific Isochorismate Synthase , 2007 .

[40]  Gideon Schreiber,et al.  Protein-protein association in polymer solutions: from dilute to semidilute to concentrated. , 2007, Biophysical journal.

[41]  G. Pielak,et al.  Macromolecular crowding fails to fold a globular protein in cells. , 2011, Journal of the American Chemical Society.

[42]  I. Nagy,et al.  Protein and water contents of aging brain. , 1982, Experimental brain research.

[43]  D. Thirumalai,et al.  Molecular crowding enhances native state stability and refolding rates of globular proteins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[44]  J. Kundu,et al.  Myoglobin unfolding in crowding and confinement. , 2012, The journal of physical chemistry. B.

[45]  M. Mayer,et al.  Hsp70 chaperones: Cellular functions and molecular mechanism , 2005, Cellular and Molecular Life Sciences.

[46]  L. Pearl,et al.  Structure of an Hsp90-Cdc37-Cdk4 complex. , 2006, Molecular cell.

[47]  A. Minton,et al.  Effect of macromolecular crowding upon the structure and function of an enzyme: glyceraldehyde-3-phosphate dehydrogenase. , 1981, Biochemistry.

[48]  A. Minton,et al.  The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media* , 2001, The Journal of Biological Chemistry.

[49]  N. Sugimoto,et al.  Study on effects of molecular crowding on G-quadruplex-ligand binding and ligand-mediated telomerase inhibition. , 2013, Methods.

[50]  Kiowa S. Bower,et al.  Accelerated α‐synuclein fibrillation in crowded milieu , 2002 .

[51]  R. Ellis,et al.  Macromolecular crowding: an important but neglected aspect of the intracellular environment. , 2001 .

[52]  Y. Sugita,et al.  Protein crowding affects hydration structure and dynamics. , 2012, Journal of the American Chemical Society.

[53]  S. Mittal,et al.  Macromolecular crowding decelerates aggregation of a β-rich protein, bovine carbonic anhydrase: a case study. , 2014, Journal of biochemistry.

[54]  R. Ellis,et al.  Protein misassembly: macromolecular crowding and molecular chaperones. , 2007, Advances in experimental medicine and biology.

[55]  Daphne H. E. W. Huberts,et al.  Macromolecular Crowding Compacts Unfolded Apoflavodoxin and Causes Severe Aggregation of the Off-pathway Intermediate during Apoflavodoxin Folding* , 2008, Journal of Biological Chemistry.

[56]  R. K. Mitra,et al.  Role of hydration on the functionality of a proteolytic enzyme α-chymotrypsin under crowded environment. , 2011, Biochimie.

[57]  Masaru Tomita,et al.  Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico , 2005, FEBS letters.

[58]  Hidekazu Hiroaki,et al.  High-resolution multi-dimensional NMR spectroscopy of proteins in human cells , 2009, Nature.

[59]  I. Zs.-Nagy,et al.  Alterations in total content and solubility characteristics of proteins in rat brain and liver during ageing and centrophenoxine treatment , 1981, Experimental Gerontology.

[60]  P. Wittung-Stafshede,et al.  Molecular crowding enhances native structure and stability of α/β protein flavodoxin , 2007, Proceedings of the National Academy of Sciences.

[61]  M. Gruebele,et al.  The extracellular protein VlsE is destabilized inside cells. , 2014, Journal of molecular biology.

[62]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[63]  C. Dobson,et al.  Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell , 2000, The EMBO journal.

[64]  H. Lilie,et al.  Identification of a redox‐regulated chaperone network , 2004, The EMBO journal.

[65]  C. Mamotte,et al.  Phenylketonuria: an inborn error of phenylalanine metabolism. , 2008, The Clinical biochemist. Reviews.

[66]  S. Mittal,et al.  Denatured State Structural Property Determines Protein Stabilization by Macromolecular Crowding: A Thermodynamic and Structural Approach , 2013, PloS one.

[67]  M. Beck,et al.  Facilitated aggregation of FG nucleoporins under molecular crowding conditions , 2013, EMBO reports.

[68]  S. Mittal,et al.  Macromolecular Crowding Induces Holo α-Lactalbumin Aggregation by Converting to Its Apo Form , 2014, PloS one.

[69]  A. Fulton,et al.  How crowded is the cytoplasm? , 1982, Cell.

[70]  F. Ahmad,et al.  Relationship between functional activity and protein stability in the presence of all classes of stabilizing osmolytes , 2009, The FEBS journal.

[71]  N. Sugimoto,et al.  Regulation of DNA nucleases by molecular crowding , 2007, Nucleic acids research.

[72]  G. Voordouw,et al.  Self‐association of the pyruvate dehydrogenase complex from Azotobacter vinelandii in the presence of polyethylene glycol , 1980, FEBS letters.

[73]  L. Pearl,et al.  Crystal structure of an Hsp90–nucleotide–p23/Sba1 closed chaperone complex , 2006, Nature.

[74]  M. Al-Habori,et al.  Macromolecular crowding and its role as intracellular signalling of cell volume regulation. , 2001, The international journal of biochemistry & cell biology.

[75]  S. Longeville,et al.  Compression of random coils due to macromolecular crowding. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[76]  Zong Lin,et al.  Effects of Macromolecular Crowding on the Unfolding and the Refolding of d-Glyceraldehyde-3-Phosophospate Dehydrogenase , 2003, Journal of protein chemistry.

[77]  T. Dar,et al.  RECENT TRENDS IN TREATING NEURONAL PROTEINOPATHIES , 2013 .

[78]  J. Clegg,et al.  Cellular and molecular consequences of reduced cell water content. , 1982, Cryobiology.

[79]  Jie Chen,et al.  Effects of macromolecular crowding on the structural stability of human α-lactalbumin. , 2012, Acta biochimica et biophysica Sinica.

[80]  Jörg Martin.  Requirement for GroEL/GroES-dependent protein folding under nonpermissive conditions of macromolecular crowding. , 2002, Biochemistry.

[81]  Vladimir N Uversky,et al.  Guiding protein aggregation with macromolecular crowding. , 2008, Biochemistry.

[82]  Mohona Sarkar,et al.  Protein crowder charge and protein stability. , 2014, Biochemistry.

[83]  D. Oesterhelt,et al.  From shell to cell: neutron scattering studies of biological water dynamics and coupling to activity. , 2009, Faraday discussions.

[84]  Jie Chen,et al.  The Role of Crowded Physiological Environments in Prion and Prion-like Protein Aggregation , 2013, International journal of molecular sciences.

[85]  C. Scholz,et al.  MiR-205 Is Progressively Down-Regulated in Lymph Node Metastasis but Fails as a Prognostic Biomarker in High-Risk Prostate Cancer , 2013, International journal of molecular sciences.

[86]  Yuji Sugita,et al.  Reduced native state stability in crowded cellular environment due to protein-protein interactions. , 2013, Journal of the American Chemical Society.

[87]  N. Malys,et al.  What is the true enzyme kinetics in the biological system? An investigation of macromolecular crowding effect upon enzyme kinetics of glucose-6-phosphate dehydrogenase. , 2011, Biochemical and biophysical research communications.

[88]  V. Bloomfield,et al.  Crowding effects on EcoRV kinetics and binding. , 1999, Biophysical journal.

[89]  R. Ellis.  Macromolecular crowding : obvious but underappreciated , 2022 .

[90]  C M Dobson,et al.  Effects of macromolecular crowding on protein folding and aggregation , 1999, The EMBO journal.

[91]  Andrew C. Miklos,et al.  Protein crowding tunes protein stability. , 2011, Journal of the American Chemical Society.

[92]  T. Dar,et al.  Ignored avenues in alpha-synuclein associated proteopathy. , 2014, CNS & neurological disorders drug targets.

[93]  M. Shirakawa,et al.  Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR. , 2013, Chemical communications.

[94]  T. Laurent,et al.  THE INTERACTION BETWEEN POLYSACCHARIDES AND OTHER MACROMOLECULES. 4. THE OSMOTIC PRESSURE OF MIXTURES OF SERUM ALBUMIN AND HYALURONIC ACID. , 1963, The Biochemical journal.

[95]  B. Korzeniewski,et al.  Dextran strongly increases the Michaelis constants of oxidative phosphorylation and of mitochondrial creatine kinase in heart mitochondria. , 1998, European journal of biochemistry.

[96]  D. Naber,et al.  Content of water-soluble and total proteins in the aging human brain , 1979, Experimental Gerontology.

[97]  N. Sugimoto,et al.  The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability. , 2004, Journal of the American Chemical Society.

[98]  A. Minton,et al.  Molecular crowding: analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion. , 1998, Methods in enzymology.

[99]  N. Faridi,et al.  The Effects of Molecular Crowding on the Amyloid Fibril Formation of α-Lactalbumin and the Chaperone Action of α-Casein , 2010, The protein journal.

[100]  Jie Chen,et al.  The Contrasting Effect of Macromolecular Crowding on Amyloid Fibril Formation , 2012, PloS one.

[101]  R. Tellam,et al.  The influence of poly(ethylene glycol) 6000 on the properties of skeletal-muscle actin. , 1983, The Biochemical journal.

[102]  N. Sugimoto,et al.  Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions. , 2006, Journal of the American Chemical Society.

[103]  P. Wittung-Stafshede,et al.  Macromolecular crowding increases structural content of folded proteins , 2007, FEBS letters.

[104]  J. J. Harding,et al.  Cataract: Biochemistry, Epidemiology and Pharmacology , 1991 .

[105]  Zoya Ignatova,et al.  From the test tube to the cell: exploring the folding and aggregation of a beta-clam protein. , 2007, Biopolymers.

[106]  C. Ross,et al.  Protein aggregation and neurodegenerative disease , 2004, Nature Medicine.

[107]  I. Kholová,et al.  Amyloid in the cardiovascular system: a review , 2005, Journal of Clinical Pathology.

[108]  Vladimir N. Uversky,et al.  Forcing Nonamyloidogenic β-Synuclein To Fibrillate† , 2005 .

[109]  Cytosol-mimetic chemistry: kinetics of the trypsin-catalyzed hydrolysis of p-nitrophenyl acetate upon addition of polyethylene glycol and N-tert-butyl acetoacetamide. , 2003, Journal of the American Chemical Society.

[110]  R. Varadarajan,et al.  Effect of crowding agents, signal peptide, and chaperone SecB on the folding and aggregation of E. coli maltose binding protein. , 2009, Langmuir : the ACS journal of surfaces and colloids.

[111]  A. Ogston.  On the interaction of solute molecules with porous networks , 1970 .

[112]  P. Mantyh,et al.  Aluminum, Iron, and Zinc Ions Promote Aggregation of Physiological Concentrations of β‐Amyloid Peptide , 1993, Journal of neurochemistry.

[113]  V. Uversky,et al.  The effect of macromolecular crowding on protein aggregation and amyloid fibril formation , 2004, Journal of molecular recognition : JMR.

[114]  P. Srere.  The infrastructure of the mitochondrial matrix , 1980 .

[115]  S. N. Olsen.  Applications of isothermal titration calorimetry to measure enzyme kinetics and activity in complex solutions , 2006 .

[116]  M. Burg.  Macromolecular Crowding as a Cell VolumeSensor , 2001, Cellular Physiology and Biochemistry.

[117]  G. Ralston.  Effects of "crowding" in protein solutions , 1990 .

[118]  Huan‐Xiang Zhou.  Polymer crowders and protein crowders act similarly on protein folding stability , 2013, FEBS letters.

[119]  A. Roque,et al.  Macromolecular crowding induces a molten globule state in the C-terminal domain of histone H1. , 2007, Biophysical journal.

[120]  A. Minton,et al.  Effect of High Concentration of Inert Cosolutes on the Refolding of an Enzyme , 2007, Journal of Biological Chemistry.

[121]  Arthur L Horwich,et al.  Chaperonin-mediated protein folding: fate of substrate polypeptide , 2003, Quarterly Reviews of Biophysics.

[122]  A. Minton,et al.  Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: macromolecular crowding and protein stability revisited. , 2005, Biophysical journal.