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Title: Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

Abstract

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature.more » This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.« less

Authors:
ORCiD logo [1];  [1];  [1];  [1];  [1];  [2];  [2]; ORCiD logo [3];  [4];  [5]; ORCiD logo [2]; ORCiD logo [1]
+ Show Author Affiliations
  1. Korea Advanced Inst. Science and Technology (KAIST), Daejeon (Korea); Inst. for Basic Science, Daejeon (Korea)
  2. Korea Advanced Inst. Science and Technology (KAIST), Daejeon (Korea)
  3. Inst. for Basic Science, Daejeon (Korea)
  4. Pohang Accelerator Lab. (PAL) (Korea)
  5. European Synchrotron Radiation Facility (ESRF), Grenoble (France)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); National Institute of General Medical Sciences (NIGMS); National Research Foundation of Korea (NRF); Institute for Basic Science (IBS)
OSTI Identifier:
1642237
Grant/Contract Number:  
AC02-06CH11357; R24GM111072
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 117; Journal Issue: 26; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
ENGLISH
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; protein folding; cytochrome c; time-resolved X-ray scattering; ensemble; molecular dynamics simulation

Citation Formats

Kim, Tae Wu, Lee, Sang Jin, Jo, Junbeom, Kim, Jong Goo, Ki, Hosung, Kim, Chang Woo, Cho, Kwang Hyun, Choi, Jungkweon, Lee, Jae Hyuk, Wulff, Michael, Rhee, Young Min, and Ihee, Hyotcherl. Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering. United States: N. p., 2020. Web. doi:10.1073/pnas.1913442117.
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Kim, Tae Wu, Lee, Sang Jin, Jo, Junbeom, Kim, Jong Goo, Ki, Hosung, Kim, Chang Woo, Cho, Kwang Hyun, Choi, Jungkweon, Lee, Jae Hyuk, Wulff, Michael, Rhee, Young Min, & Ihee, Hyotcherl. Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering. United States. https://doi.org/10.1073/pnas.1913442117
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Kim, Tae Wu, Lee, Sang Jin, Jo, Junbeom, Kim, Jong Goo, Ki, Hosung, Kim, Chang Woo, Cho, Kwang Hyun, Choi, Jungkweon, Lee, Jae Hyuk, Wulff, Michael, Rhee, Young Min, and Ihee, Hyotcherl. Mon . "Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering". United States. https://doi.org/10.1073/pnas.1913442117. https://www.osti.gov/servlets/purl/1642237.
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@article{osti_1642237,
title = {Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering},
author = {Kim, Tae Wu and Lee, Sang Jin and Jo, Junbeom and Kim, Jong Goo and Ki, Hosung and Kim, Chang Woo and Cho, Kwang Hyun and Choi, Jungkweon and Lee, Jae Hyuk and Wulff, Michael and Rhee, Young Min and Ihee, Hyotcherl},
abstractNote = {One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.},
doi = {10.1073/pnas.1913442117},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 26,
volume = 117,
place = {United States},
year = {Mon Jun 15 00:00:00 EDT 2020},
month = {Mon Jun 15 00:00:00 EDT 2020}
}
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https://doi.org/10.1073/pnas.1913442117
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Figures / Tables:

Fig. 1 Fig. 1: Free-energy landscapes induced by external electron injection. Conventional free-energy surfaces for two different conditions as a function of representative reaction coordinates ($q$1 and $q$2). The reaction coordinates correspond to local structural changes in protein such as vibrational modes of specific residues or distances between residues. The free-energy surfacemore » can be resculpted by the change in protein environment, indicated as the yellow arrow, such as oxidation state of cofactor and solvent condition. From this, the basin of the unfolded state in the free-energy surface (Bottom) changes as a hillside in the resculpted energy surface (Top). The change of energetics activates the spontaneous folding pathways, indicated as the magenta arrow, along the reaction coordinates. As indicated with the gray dotted arrow, the pathway is inhibited in the initial condition.« less
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