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A survey of lambda repressor fragments from two-state to downhill folding.

Liu F, Gao YG, Gruebele M
J Mol Biol 397 789-98 (2010)
Cited: 26 times
EuropePMC logo PMID: 20138892

Abstract

We survey the two-state to downhill folding transition by examining 20 lambda(6-85)* mutants that cover a wide range of stabilities and folding rates. We investigated four new lambda(6-85)* mutants designed to fold especially rapidly. Two were engineered using the core remodeling of Lim and Sauer, and two were engineered using Ferreiro et al.'s frustratometer. These proteins have probe-dependent melting temperatures as high as 80 degrees C and exhibit a fast molecular phase with the characteristic temperature dependence of the amplitude expected for downhill folding. The survey reveals a correlation between melting temperature and downhill folding previously observed for the beta-sheet protein WW domain. A simple model explains this correlation and predicts the melting temperature at which downhill folding becomes possible. An X-ray crystal structure with a 1.64-A resolution of a fast-folding mutant fragment shows regions of enhanced rigidity compared to the full wild-type protein.

Reviews - 3kz3 mentioned but not cited (1)

  1. Fast protein folding kinetics. Gelman H, Gruebele M. Q Rev Biophys 47 95-142 (2014)

Articles - 3kz3 mentioned but not cited (12)

  1. Misplaced helix slows down ultrafast pressure-jump protein folding. Prigozhin MB, Liu Y, Wirth AJ, Kapoor S, Winter R, Schulten K, Gruebele M. Proc Natl Acad Sci U S A 110 8087-8092 (2013)
  2. A survey of lambda repressor fragments from two-state to downhill folding. Liu F, Gao YG, Gruebele M. J Mol Biol 397 789-798 (2010)
  3. Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations. Liu Y, Strümpfer J, Freddolino PL, Gruebele M, Schulten K. J Phys Chem Lett 3 1117-1123 (2012)
  4. Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment. Liu Y, Prigozhin MB, Schulten K, Gruebele M. J Am Chem Soc 136 4265-4272 (2014)
  5. Mapping fast protein folding with multiple-site fluorescent probes. Prigozhin MB, Chao SH, Sukenik S, Pogorelov TV, Gruebele M. Proc Natl Acad Sci U S A 112 7966-7971 (2015)
  6. Engineering folding dynamics from two-state to downhill: application to λ-repressor. Carter JW, Baker CM, Best RB, De Sancho D. J Phys Chem B 117 13435-13443 (2013)
  7. Dodine as a protein denaturant: the best of two worlds? Gelman H, Perlova T, Gruebele M. J Phys Chem B 117 13090-13097 (2013)
  8. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. Cieplak AS. PLoS One 12 e0180905 (2017)
  9. Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange. Yu W, Baxa MC, Gagnon I, Freed KF, Sosnick TR. Proc Natl Acad Sci U S A 113 4747-4752 (2016)
  10. The Surface of Protein λ6-85 Can Act as a Template for Recurring Poly(ethylene glycol) Structure. Chao SH, Schäfer J, Gruebele M. Biochemistry 56 5671-5678 (2017)
  11. Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics. Prigozhin MB, Zhang Y, Schulten K, Gruebele M, Pogorelov TV. Proc Natl Acad Sci U S A 116 5356-5361 (2019)
  12. Machine learning coarse-grained potentials of protein thermodynamics. Majewski M, Pérez A, Thölke P, Doerr S, Charron NE, Giorgino T, Husic BE, Clementi C, Noé F, De Fabritiis G. Nat Commun 14 5739 (2023)


Reviews citing this publication (2)

  1. The folding of single domain proteins--have we reached a consensus? Sosnick TR, Barrick D. Curr Opin Struct Biol 21 12-24 (2011)
  2. How cooperative are protein folding and unfolding transitions? Malhotra P, Udgaonkar JB. Protein Sci 25 1924-1941 (2016)

Articles citing this publication (11)

  1. Challenges in protein folding simulations: Timescale, representation, and analysis. Freddolino PL, Harrison CB, Liu Y, Schulten K. Nat Phys 6 751-758 (2010)
  2. Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. Shirvanyants D, Ding F, Tsao D, Ramachandran S, Dokholyan NV. J Phys Chem B 116 8375-8382 (2012)
  3. Atomistic folding simulations of the five-helix bundle protein λ(6−85). Bowman GR, Voelz VA, Pande VS. J Am Chem Soc 133 664-667 (2011)
  4. Globular Protein Folding In Vitro and In Vivo. Gruebele M, Dave K, Sukenik S. Annu Rev Biophys 45 233-251 (2016)
  5. The fast and the slow: folding and trapping of λ6-85. Prigozhin MB, Gruebele M. J Am Chem Soc 133 19338-19341 (2011)
  6. Rapid perturbation of free-energy landscapes: from in vitro to in vivo. Gelman H, Platkov M, Gruebele M. Chemistry 18 6420-6427 (2012)
  7. Sequence, structure, and cooperativity in folding of elementary protein structural motifs. Lai JK, Kubelka GS, Kubelka J. Proc Natl Acad Sci U S A 112 9890-9895 (2015)
  8. Crowding effects on the small, fast-folding protein lambda6-85. Denos S, Dhar A, Gruebele M. Faraday Discuss 157 451-62; discussion 475-500 (2012)
  9. Equilibrium unfolding of the PDZ domain of β2-syntrophin. Torchio GM, Ermácora MR, Sica MP. Biophys J 102 2835-2844 (2012)
  10. Co-translational folding of α-helical proteins: structural studies of intermediate-length variants of the λ repressor. Hanazono Y, Takeda K, Miki K. FEBS Open Bio 8 1312-1321 (2018)
  11. Molecular dynamics approach to understand the denaturing effect of a millimolar concentration of dodine on a λ-repressor and counteraction by trehalose. Borgohain G, Mandal B, Paul S. Phys Chem Chem Phys 19 13160-13171 (2017)


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