The effects of volume exclusion and viscosity on collagen fiber nucleation and network morphology
Source abstract
Abstract
Protein behavior, including protein-protein association and self-assembly, differs in dilute buffers compared to in the crowded environments that are typical in vivo. We performed a comprehensive study of the impacts of crowding on collagen self-assembly into fibers using a range of polysaccharides and polyethylene glycols (PEG) at volume fractions in the physiological range as well as small molecule analogues of these species. We find that crowding accelerates collagen fiber nucleation in proportion to excluded volume without changes to collagen secondary structure or thermal stability, with the acceleration greater for PEGs than for polysaccharides at the same volume fraction. Additionally, we observed the competing effects of volume fraction and viscosity on nucleation, with volume fraction dominant in setting the collagen fiber nucleation time at high degrees of crowding. We show, consistent with previous findings on collagen gelation as a function of temperature, that fiber and network morphological and mechanical differences in collagen gels formed from these solutions is determined primarily by changes in nucleation time, with short nucleation times leading to softer collagen networks with abundant, thin fibers and long nucleation times resulting in stiffer networks with sparse, thick fiber bundles. STATEMENT OF SIGNIFICANCE: We studied the effects of several macromolecules and small molecule analogues on collagen self-assembly and the resulting fiber and network properties of collagen gels. We observed competing effects of excluded volume and viscosity on collagen nucleation depending on the volume fraction of the co-solute and assert that the morphological changes in the resulting gels are due to changes to nucleation time alone. This work elucidates the various effects of co-solutes on collagen self-assembly and is of use for control of collagen material properties and for understanding crowding and related effects on other self-associating proteins.
Source: europepmc · Quality: candidate unverified · Source record ↗
Research context
OpenAlex topics: Collagen: Extraction and Characterization · Advanced Biosensing Techniques and Applications · Hydrogels: synthesis, properties, applications
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
References (99)
Show source-provided references
1. How crowded is the cytoplasm?10.1016/0092-8674(82)90231-8 ↗
2. Diffusion in brain extracellular space10.1152/physrev.00027.2007 ↗
3. Protein folding dynamics in the cell10.1021/jp501866v ↗
4. The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological Media10.1074/jbc.R100005200 ↗
5. Macromolecular crowding: biochemical, biophysical, and physiological consequences10.1146/annurev.bb.22.060193.000331 ↗
6. Extracellular space structure revealed by diffusion analysis10.1016/S0166-2236(98)01261-2 ↗
7. The extracellular matrix at a glance10.1242/jcs.023820 ↗
8. Extracellular matrix assembly: a multiscale deconstruction10.1038/nrm3902 ↗
9. The extracellular matrix In development and morphogenesis: a dynamic view10.1016/j.ydbio.2009.10.026 ↗
10. The extracellular matrix as a multitasking player in disease10.1111/febs.14818 ↗
11. The mechanics of fibrillar collagen extracellular matrix
12. Macromolecular crowding directs extracellular matrix organization and mesenchymal stem cell behavior10.1371/journal.pone.0037904 ↗
13. Macromolecularly crowded in vitro microenvironments accelerate the production of extracellular matrix-rich supramolecular assemblies10.1038/srep08729 ↗
14. Applying macromolecular crowding to enhance extracellular matrix deposition and its remodeling in vitro for tissue engineering and cell-based therapies10.1016/j.addr.2011.03.003 ↗
15. Carrageenan as a macromolecular crowding agent in human umbilical cord derived mesenchymal stromal cell culture10.1016/j.ijbiomac.2023.126353 ↗
16. Cleavage of type I procollagen by C- and N-proteinases is more rapid if the substrate is aggregated with dextran sulfate or polyethylene glycol10.1006/abio.1994.1569 ↗
17. Collagen matrix deposition is dramatically enhanced in vitro when crowded with charged macromolecules: the biological relevance of the excluded volume effect10.1016/j.febslet.2007.05.020 ↗
18. Macromolecular crowding regulates matrix composition and gene expression in human gingival fibroblast cultures10.1038/s41598-023-29252-1 ↗
19. Macromolecular crowding meets tissue engineering by self-assembly: a paradigm shift in regenerative medicine10.1002/adma.201304428 ↗
20. Extracellular matrix deposition of bone marrow stroma enhanced by macromolecular crowding10.1016/j.biomaterials.2015.09.014 ↗
21. Fibrillar fibronectin plays a key role as nucleator of collagen I polymerization during macromolecular crowding-enhanced matrix assembly10.1039/C9BM00868C ↗
22. Direct observation of the self-association of dilute proteins in the presence of inert macromolecules at high concentration via tracer sedimentation equilibrium: theory, experiment, and biological significance10.1021/bi990355z ↗
23. Local nucleation of microtubule bundles through tubulin concentration into a condensed tau phase10.1016/j.celrep.2017.08.042 ↗
24. Macromolecular crowding gives rise to microviscosity, anomalous diffusion and accelerated actin polymerization10.1088/1478-3975/12/3/034001 ↗
25. Macromolecular crowding accelerates amyloid formation by Human apolipoprotein C-II *10.1074/jbc.M110429200 ↗
26. The effect of macromolecular crowding on protein aggregation and amyloid fibril formation10.1002/jmr.699 ↗
27. Macromolecular crowding as a suppressor of Human IAPP fibril formation and cytotoxicity10.1371/journal.pone.0069652 ↗
28. Molecular crowding of collagen: a pathway to produce highly-organized collagenous structures10.1016/j.biomaterials.2012.06.041 ↗
29. Tuning the architecture of three-dimensional collagen hydrogels by physiological macromolecular crowding10.1016/j.actbio.2014.06.006 ↗
30. Macromolecular crowding tunes 3D collagen architecture and cell morphogenesis10.1039/C8BM01188E ↗
31. Sugars and polyols inhibit fibrillogenesis of type I collagen by disrupting hydrogen-bonded water bridges between the helices10.1021/bi980089+ ↗
32. Correlation between collagen solubility and skin optical clearing using sugars10.1002/lsm.20417 ↗
33. Improvement of collagen self-assembly and thermal stability in the presence of trehalose10.1039/D2NJ00677D ↗
34. Physical properties of type i collagen in solution: structure of α-chains and β- and γ-components and two-component mixtures10.1002/bip.1981.360200208 ↗
35. Translational and rotational dynamics of collagen in dilute solution10.1021/jp961607y ↗
36. Type I collagen in solution. Structure and properties of fibril fragments10.1016/S0021-9258(19)70580-8 ↗
37. Molecular structure of collagen in solution: comparison of types I, II, III and V10.1016/0141-8130(84)90052-7 ↗
38. Advances in bioconjugation10.2174/138527210790069839 ↗
39. Collagen I self-assembly: revealing the developing structures that generate turbidity10.1016/j.bpj.2014.03.011 ↗
40. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration10.1073/pnas.2313162121 ↗
41. Kinetic analysis of collagen fibrillogenesis: I. Use of turbidity–time data10.1016/S0174-173X(83)80020-X ↗
42. Confocal rheology probes the structure and mechanics of collagen through the sol-gel transition10.1016/j.bpj.2017.08.025 ↗
43. Elongation of actin filaments is a diffusion-limited reaction at the barbed end and is accelerated by inert macromolecules10.1016/S0021-9258(18)67157-1 ↗
44. Macromolecular crowding: an important but neglected aspect of the intracellular environment10.1016/S0959-440X(00)00172-X ↗
45. Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells10.1529/biophysj.104.044263 ↗
46. Elastic moduli of collagen gels can Be predicted from two-dimensional confocal microscopy10.1016/j.bpj.2009.07.035 ↗
47. Pore size variable type I collagen gels and their interaction with glioma cells10.1016/j.biomaterials.2010.03.039 ↗
48. Crowding alone cannot account for cosolute effect on amyloid aggregation10.1371/journal.pone.0015608 ↗
49. Mechanism for retardation of amyloid fibril formation by sugars in Vλ6 protein10.1002/pro.2228 ↗
50. Sucrose modulates insulin amyloid-like fibril formation: effect on the aggregation mechanism and fibril morphology10.1039/C6RA25872G ↗
51. Polyol and sugar osmolytes stabilize the molten globule state of α-lactalbumin and inhibit amyloid fibril formation10.1016/j.bbapap.2022.140853 ↗
52. Macromolecular crowding modulates α-synuclein amyloid fiber growth10.1016/j.bpj.2021.06.032 ↗
53. Protein folding by the effects of macromolecular crowding10.1110/ps.03288104 ↗
54. Molecular crowding enhances native state stability and refolding rates of globular proteins10.1073/pnas.0409630102 ↗
55. Molecular crowding enhances native structure and stability of α/β protein flavodoxin10.1073/pnas.0705127104 ↗
56. Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded State10.1021/ja103166y ↗
57. Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding10.1073/pnas.1006760107 ↗
58. Type I collagen is thermally unstable at body temperature10.1073/pnas.032307099 ↗
59. Altered collagen structure in mouse tail tendon lacking the α2(I) chain110.1006/jmbi.1997.1106 ↗
60. C.A. Tobita, S. Banerjee, J. Roth, E.K. Larson, A. Nikzad, A. Naiyer, C.L. Hoop, J. Baum, Nanoscale structural and functional impacts of disease-associated collagen mutations, (2025) 2025.09.03.673992. https://doi.org/10.1101/2025.09.03.673992.10.1101/2025.09.03.673992 ↗
61. Development of fluorescently labeled, functional type I collagen molecules10.1002/mabi.202100144 ↗
62. Noninvasive assessment of collagen gel microstructure and mechanics using multiphoton microscopy10.1529/biophysj.106.097998 ↗
63. Collagen oligomers modulate physical and biological properties of three-dimensional self-assembled matrices10.1002/bip.21537 ↗
64. Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges10.1016/S1570-9639(03)00167-5 ↗
65. The effect of volume occupancy upon the thermodynamic activity of proteins: some biochemical consequences10.1007/BF00673707 ↗
66. Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli10.1016/0022-2836(91)90499-V ↗
67. Implications of macromolecular crowding for protein assembly10.1016/S0959-440X(99)00045-7 ↗
68. Effects of inert volume-excluding macromolecules on protein fiber formation. I. Equilibrium models10.1016/S0301-4622(02)00087-X ↗
69. Effect of inert polymers on protein self-association10.1016/0014-5793(81)81022-8 ↗
70. Crowding induced collective hydration of biological macromolecules over extended distances10.1021/ja407858c ↗
71. Quantitative assessment of the relative contributions of steric repulsion and chemical interactions to macromolecular crowding10.1002/bip.22163 ↗
72. Soft interactions and crowding10.1007/s12551-013-0104-4 ↗
73. Protein stabilization by macromolecular crowding through enthalpy rather than entropy10.1021/ja503205y ↗
74. Macromolecular crowding is more than hard-core repulsions10.1146/annurev-biophys-091321-071829 ↗
75. Protein crowding affects hydration structure and dynamics10.1021/ja211115q ↗
76. Role of associated water dynamics on protein stability and activity in crowded milieu10.1021/acs.jpcb.4c04337 ↗
77. Dominant forces in protein folding10.1021/bi00483a001 ↗
78. Protein folding under confinement: a role for solvent10.1073/pnas.0608256104 ↗
79. Water determines the structure and dynamics of proteins10.1021/acs.chemrev.5b00664 ↗
80. Associated water dynamics might Be a key factor affecting protein stability in the crowded milieu10.1021/acs.jpcb.2c09043 ↗
81. Circular dichroism spectroscopy of membrane proteins10.1039/C5CS00084J ↗
82. Hydration structure of a collagen peptide10.1016/S0969-2126(01)00224-6 ↗
83. Raman spectral evidence for hydration forces between collagen triple helices10.1073/pnas.94.21.11312 ↗
84. Do macromolecular crowding agents exert only an excluded volume effect? A protein solvation study10.1021/acs.jpcb.5b09446 ↗
85. Shape-dependent macromolecular crowding on the thermodynamics and microsecond conformational dynamics of protein unfolding revealed at the single-molecule level10.1021/acs.jpcb.0c03897 ↗
86. Role of hydration on the functionality of a proteolytic enzyme α-chymotrypsin under crowded environment10.1016/j.biochi.2011.04.017 ↗
87. The role of water in reactions catalysed by hydrolases under conditions of molecular crowding10.1007/s12551-023-01104-2 ↗
88. Molecular dynamics simulations on aqueous two-phase systems - single PEG-molecules in solution10.1186/2046-1682-5-14 ↗
89. The formation of fibrils from collagen solutions. 1. The effect of experimental conditions: kinetic and electron-microscope studies10.1042/bj0750588 ↗
90. Strain stiffening in collagen I networks10.1002/bip.22133 ↗
91. Plasticity variable collagen-PEG interpenetrating networks modulate cell spreading10.1016/j.actbio.2024.08.040 ↗
92. Instant assembly of collagen for tissue engineering and bioprinting10.1038/s41563-025-02241-7 ↗
93. Principles of protein folding, misfolding and aggregation10.1016/j.semcdb.2003.12.008 ↗
94. Guiding protein aggregation with macromolecular crowding10.1021/bi8008399 ↗
95. The contrasting effect of macromolecular crowding on amyloid fibril formation
96. Protein aggregation kinetics, mechanism, and curve-fitting: a review of the literature10.1016/j.bbapap.2008.10.016 ↗
97. Modelling amyloid fibril formation kinetics: mechanisms of nucleation and growth10.1088/0953-8984/25/37/373101 ↗
98. Crowding effects on amyloid aggregation kinetics10.1021/jz100967z ↗
99. Effects of macromolecular crowding on amyloid beta (16–22) aggregation using coarse-grained simulations10.1021/jp508970q ↗