TY - JOUR
T1 - Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random coil-like dimensions
AU - Peran, Ivan
AU - Holehouse, Alex S.
AU - Carrico, Isaac S.
AU - Pappu, Rohit V.
AU - Bilsel, Osman
AU - Raleigh, Daniel P.
N1 - Funding Information:
ACKNOWLEDGMENTS. This work was supported by Wellcome Trust Grant 107927/Z/15/Z (to D.P.R.), the US National Science Foundation (NSF) Grants IDBR 1353942 and MCB 0721312 (to O.B.) and MCB-1614766 (to R.V.P.), and the Human Frontiers Science Program Grant RGP0034/2017 (to R.V.P.). I.P. was supported in part by NSF Grant MCB-1330259 (to D.P.R.). O.B., R.V.P., and D.P.R. are members of the protein-folding consortium that is supported by the NSF through Grant MCB 1051344. We thank S. Chakravarthy and S. V. Kathuria for assistance with SAXS measurements. We are grateful to current and former members of the O.B., R.V.P., and D.P.R. laboratories as well as Prof. C. R. Matthews for helpful discussions. This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357. This project was supported by Grant 9 P41 GM103622 from the National Institute of General Medical Sciences of the National Institutes of Health.
Funding Information:
This work was supported by Wellcome Trust Grant 107927/Z/15/Z (to D.P.R.), the US National Science Foundation (NSF) Grants IDBR 1353942 and MCB 0721312 (to O.B.) and MCB-1614766 (to R.V.P.), and the Human Frontiers Science Program Grant RGP0034/2017 (to R.V.P.). I.P. was supported in part by NSF Grant MCB-1330259 (to D.P.R.). O.B., R.V.P., and D.P.R. are members of the protein-folding consortium that is supported by the NSF through Grant MCB 1051344. We thank S. Chakravarthy and S. V. Kathuria for assistance with SAXS measurements. We are grateful to current and former members of the O.B., R.V.P., and D.P.R. laboratories as well as Prof. C. R. Matthews for helpful discussions. This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357. This project was supported by Grant 9 P41 GM103622 from the National Institute of General Medical Sciences of the National Institutes of Health.
Publisher Copyright:
© 2019 National Academy of Sciences. All rights reserved.
PY - 2019/6/18
Y1 - 2019/6/18
N2 - Proteins are marginally stable molecules that fluctuate between folded and unfolded states. Here, we provide a high-resolution description of unfolded states under refolding conditions for the N-terminal domain of the L9 protein (NTL9). We use a combination of time-resolved Förster resonance energy transfer (FRET) based on multiple pairs of minimally perturbing labels, time-resolved small-angle X-ray scattering (SAXS), all-atom simulations, and polymer theory. Upon dilution from high denaturant, the unfolded state undergoes rapid contraction. Although this contraction occurs before the folding transition, the unfolded state remains considerably more expanded than the folded state and accommodates a range of local and nonlocal contacts, including secondary structures and native and nonnative interactions. Paradoxically, despite discernible sequence-specific conformational preferences, the ensemble-averaged properties of unfolded states are consistent with those of canonical random coils, namely polymers in indifferent (theta) solvents. These findings are concordant with theoretical predictions based on coarse-grained models and inferences drawn from single-molecule experiments regarding the sequence-specific scaling behavior of unfolded proteins under folding conditions.
AB - Proteins are marginally stable molecules that fluctuate between folded and unfolded states. Here, we provide a high-resolution description of unfolded states under refolding conditions for the N-terminal domain of the L9 protein (NTL9). We use a combination of time-resolved Förster resonance energy transfer (FRET) based on multiple pairs of minimally perturbing labels, time-resolved small-angle X-ray scattering (SAXS), all-atom simulations, and polymer theory. Upon dilution from high denaturant, the unfolded state undergoes rapid contraction. Although this contraction occurs before the folding transition, the unfolded state remains considerably more expanded than the folded state and accommodates a range of local and nonlocal contacts, including secondary structures and native and nonnative interactions. Paradoxically, despite discernible sequence-specific conformational preferences, the ensemble-averaged properties of unfolded states are consistent with those of canonical random coils, namely polymers in indifferent (theta) solvents. These findings are concordant with theoretical predictions based on coarse-grained models and inferences drawn from single-molecule experiments regarding the sequence-specific scaling behavior of unfolded proteins under folding conditions.
KW - Compaction transition
KW - FRET
KW - Protein folding
KW - Unfolded state
UR - http://www.scopus.com/inward/record.url?scp=85067606075&partnerID=8YFLogxK
U2 - 10.1073/pnas.1818206116
DO - 10.1073/pnas.1818206116
M3 - Article
C2 - 31167941
AN - SCOPUS:85067606075
SN - 0027-8424
VL - 116
SP - 12301
EP - 12310
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 25
ER -