Biomolecules inhabit a crowded living cell that is packed with high concentrations of cosolutes and macromolecules that result in restricted, confined volumes for biomolecular dynamics. To understand the impact of crowding on the biomolecular structure, the combined effects of the cosolutes (such as urea) and confinement need to be accounted for. This study involves examining these effects on the collapse equilibria of three model 32-mer polymers, which are simplified models of hydrophobic, charge-neutral, and uncharged hydrophilic polymers, using molecular dynamics simulations. The introduction of confinement promotes the collapse of all three polymers. Interestingly, addition of urea weakens the collapse of the confined hydrophobic polymer, leading to non-additive effects, whereas for the hydrophilic polymers, urea enhances the confinement effects by enhancing polymer collapse (or decreasing the polymer unfolding), thereby exhibiting an additive effect. The unfavorable dehydration energy opposes collapse in the confined hydrophobic and charge-neutral polymers under the influence of urea. However, the collapse is driven mainly by the favorable change in polymer–solvent entropy. The confined hydrophilic polymer, which tends to unfold in bulk water, is seen to have reduced unfolding in the presence of urea due to the stabilizing of the collapsed state by urea via cohesive bridging interactions. Therefore, there is a complex balance of competing factors, such as polymer chemistry and polymer–water and polymer–cosolute interactions, beyond volume exclusion effects, which determine the collapse equilibria under confinement. The results have implications to understand the altering of the free energy landscape of proteins in the confined living cell environment.
REFERENCES
1.
R. J.
Ellis
, “Macromolecular crowding: Obvious but underappreciated
,” Trends Biochem. Sci.
26
, 597
–604
(2001
).2.
A. P.
Minton
and J.
Wilf
, “Effect of macromolecular crowding upon the structure and function of an enzyme: Glyceraldehyde-3-phosphate dehydrogenase
,” Biochemistry
20
, 4821
–4826
(1981
).3.
R. J.
Ellis
and A. P.
Minton
, “Cell biology: Join the crowd
,” Nature
425
, 27
–28
(2003
).4.
S.
Asakura
and F.
Oosawa
, “On interaction between two bodies immersed in a solution of macromolecules
,” J. Chem. Phys.
22
, 1255
–1256
(1954
).5.
S.
Asakura
and F.
Oosawa
, “Interaction between particles suspended in solutions of macromolecules
,” J. Polym. Sci.
33
, 183
–192
(1958
).6.
E. J.
Meijer
and D.
Frenkel
, “Colloids dispersed in polymer solutions. A computer simulation study
,” J. Chem. Phys.
100
, 6873
–6887
(1994
).7.
H.-X.
Zhou
, G.
Rivas
, and A. P.
Minton
, “Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences
,” Annu. Rev. Biophys.
37
, 375
–397
(2008
).8.
K. A.
Sharp
, “Analysis of the size dependence of macromolecular crowding shows that smaller is better
,” Proc. Natl. Acad. Sci. U. S. A.
112
, 7990
–7995
(2015
).9.
M. R.
Hilaire
, R. M.
Abaskharon
, and F.
Gai
, “Biomolecular crowding arising from small molecules, molecular constraints, surface packing, and nano-confinement
,” J. Phys. Chem. Lett.
6
, 2546
–2553
(2015
).10.
M.
Senske
, L.
Törk
, B.
Born
, M.
Havenith
, C.
Herrmann
, and S.
Ebbinghaus
, “Protein stabilization by macromolecular crowding through enthalpy rather than entropy
,” J. Am. Chem. Soc.
136
, 9036
–9041
(2014
).11.
D.
Nayar
, “Small crowder interactions can drive hydrophobic polymer collapse as well as unfolding
,” Phys. Chem. Chem. Phys.
22
, 18091
–18101
(2020
).12.
D.
Nayar
, “Molecular crowders can induce collapse in hydrophilic polymers via soft attractive interactions
,” J. Phys. Chem. B
127
, 6265
–6276
(2023
).13.
M.
Sarkar
, C.
Li
, and G. J.
Pielak
, “Soft interactions and crowding
,” Biophys. Rev.
5
, 187
–194
(2013
).14.
S. K.
Mukherjee
, S.
Gautam
, S.
Biswas
, J.
Kundu
, and P. K.
Chowdhury
, “Do macromolecular crowding agents exert only an excluded volume effect? A protein solvation study
,” J. Phys. Chem. B
119
, 14145
–14156
(2015
).15.
S. L.
Speer
, C. J.
Stewart
, L.
Sapir
, D.
Harries
, and G. J.
Pielak
, “Macromolecular crowding is more than hard-core repulsions
,” Annu. Rev. Biophys.
51
, 267
–300
(2022
).16.
C.
Alfano
, Y.
Fichou
, K.
Huber
, M.
Weiss
, E.
Spruijt
, S.
Ebbinghaus
, G.
De Luca
, M. A.
Morando
, V.
Vetri
, P. A.
Temussi
, and A.
Pastore
, “Molecular crowding: The history and development of a scientific paradigm
,” Chem. Rev.
124
, 3186
–3219
(2024
).17.
H. S.
Chan
and K. A.
Dill
, “A simple model of chaperonin-mediated protein folding
,” Proteins: Struct., Funct., Bioinf.
24
, 345
–351
(1996
).18.
P.
Nissen
, J.
Hansen
, N.
Ban
, P. B.
Moore
, and T. A.
Steitz
, “The structural basis of ribosome activity in peptide bond synthesis
,” Science
289
, 920
–930
(2000
).19.
T.
Misteli
, “Beyond the sequence: Cellular organization of genome function
,” Cell
128
, 787
–800
(2007
).20.
D. R.
Canchi
and A. E.
García
, “Cosolvent effects on protein stability
,” Annu. Rev. Phys. Chem.
64
, 273
–293
(2013
).21.
S. S.
Cho
, G.
Reddy
, J. E.
Straub
, and D.
Thirumalai
, “Entropic stabilization of proteins by TMAO
,” J. Phys. Chem. B
115
, 13401
–13407
(2011
).22.
J. K.
Chung
, M. C.
Thielges
, and M. D.
Fayer
, “Conformational dynamics and stability of HP35 studied with 2D IR vibrational echoes
,” J. Am. Chem. Soc.
134
, 12118
–12124
(2012
).23.
E. D.
Holmstrom
, N. F.
Dupuis
, and D. J.
Nesbitt
, “Kinetic and thermodynamic origins of osmolyte-influenced nucleic acid folding
,” J. Phys. Chem. B
119
, 3687
–3696
(2015
).24.
R. M.
Culik
, R. M.
Abaskharon
, I. M.
Pazos
, and F.
Gai
, “Experimental validation of the role of trifluoroethanol as a nanocrowder
,” J. Phys. Chem. B
118
, 11455
–11461
(2014
).25.
A.
Maity
, S.
Sarkar
, L.
Theeyancheri
, and R.
Chakrabarti
, “Choline chloride as a nano-crowder protects HP-36 from urea-induced denaturation: Insights from solvent dynamics and protein-solvent interactions
,” ChemPhysChem
21
, 552
–567
(2020
).26.
N. F. A.
van der Vegt
and D.
Nayar
, “The hydrophobic effect and the role of cosolvents
,” J. Phys. Chem. B
121
, 9986
–9998
(2017
).27.
N. F. A.
van der Vegt
, “Length-scale effects in hydrophobic polymer collapse transitions
,” J. Phys. Chem. B
125
, 5191
–5199
(2021
).28.
L. B.
Sagle
, Y.
Zhang
, V. A.
Litosh
, X.
Chen
, Y.
Cho
, and P. S.
Cremer
, “Investigating the hydrogen-bonding model of urea denaturation
,” J. Am. Chem. Soc.
131
, 9304
–9310
(2009
).29.
J.
Wang
, B.
Liu
, G.
Ru
, J.
Bai
, and J.
Feng
, Macromolecules
49
, 234
–243
(2016
).30.
D.
Nayar
, A.
Folberth
, and N. F. A.
van der Vegt
, “Molecular origin of urea driven hydrophobic polymer collapse and unfolding depending on side chain chemistry
,” Phys. Chem. Chem. Phys.
19
, 18156
–18161
(2017
).31.
D.
Nayar
and N. F. A.
van der Vegt
, “Cosolvent effects on polymer hydration drive hydrophobic collapse
,” J. Phys. Chem. B
122
, 3587
–3595
(2018
).32.
J.
Mittal
and R. B.
Best
, “Thermodynamics and kinetics of protein folding under confinement
,” Proc. Natl. Acad. Sci. U. S. A.
105
, 20233
–20238
(2008
).33.
A.
Bhattacharya
, R. B.
Best
, and J.
Mittal
, “Smoothing of the GB1 hairpin folding landscape by interfacial confinement
,” Biophys. J.
103
, 596
–600
(2012
).34.
J.
Tian
and A. E.
Garcia
, “Simulation studies of protein folding/unfolding equilibrium under polar and nonpolar confinement
,” J. Am. Chem. Soc.
133
, 15157
–15164
(2011
).35.
Z.
Cai
and Y.
Zhang
, “Hydrophobicity-driven unfolding of Trp-cage encapsulated between graphene sheets
,” Colloids Surf., B
168
, 103
–108
(2018
).36.
K. A.
Marino
and P. G.
Bolhuis
, “Confinement-induced states in the folding landscape of the Trp-cage miniprotein
,” J. Phys. Chem. B
116
, 11872
–11880
(2012
).37.
K.
Tripathi
, G. I.
Menon
, and S.
Vemparala
, “Confined crowded polymers near attractive surfaces
,” J. Chem. Phys.
151
, 244901
(2019
).38.
B.
Widom
, “Some topics in the theory of fluids
,” J. Chem. Phys.
39
, 2808
–2812
(1963
).39.
R.
Zangi
, R.
Zhou
, and B. J.
Berne
, “Urea’s action on hydrophobic interactions
,” J. Am. Chem. Soc.
131
, 1535
–1541
(2009
).40.
M.
Mukherjee
and J.
Mondal
, “Osmolyte-induced collapse of a charged macromolecule
,” J. Phys. Chem. B
123
, 4636
–4644
(2019
).41.
S.
Weerasinghe
and P. E.
Smith
, “A Kirkwood–Buff derived force field for mixtures of urea and water
,” J. Phys. Chem. B
107
, 3891
–3898
(2003
).42.
B.
Hess
, C.
Kutzner
, D.
van der Spoel
, and E.
Lindahl
, “GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
,” J. Chem. Theory Comput.
4
, 435
–447
(2008
).43.
G. A.
Tribello
, M.
Bonomi
, D.
Branduardi
, C.
Camilloni
, and G.
Bussi
, “PLUMED 2: New feathers for an old bird
,” Comput. Phys. Commun.
185
, 604
–613
(2014
).44.
S.
Kumar
, J. M.
Rosenberg
, D.
Bouzida
, R. H.
Swendsen
, and P. A.
Kollman
, “The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
,” J. Comput. Chem.
13
, 1011
–1021
(1992
).45.
V.
Pierce
, M.
Kang
, M.
Aburi
, S.
Weerasinghe
, and P.
Smith
, “Recent applications of Kirkwood-Buff theory to biological systems
,” Cell Biochem. Biophys.
50
, 1
–22
(2008
).46.
S.
Mukherjee
, P.
Chowdhury
, and F.
Gai
, “Tuning the cooperativity of the helix–coil transition by aqueous reverse micelles
,” J. Phys. Chem. B
110
, 11615
–11619
(2006
).© 2024 Author(s). Published under an exclusive license by AIP Publishing.
2024
Author(s)
You do not currently have access to this content.
