, REFERENCES Biophys. Chem. Rouget, J. B J, vol.159, issue.123, p.217, 1995.
, J. Am. Chem. Soc, vol.133, pp.6020-6024, 2011.
, Proc. Natl. Acad. Sci. U. S. A. 201210) Lin, L. N.; Brandts, J. F.; Brandts, J. M.; Plotnikov, V. Anal, pp.6945-346, 1038.
, Biochem J. Phys. Chem. B M.; Kobayashi, K.; Rouget, J. B J. A. J, vol.302, issue.11412, pp.144-16166, 2002.
, J. Phys
, Chem. B 2013, vol.117, p.12742
Article DOI: 10.1021/jacs, Journal of the American Chemical Society J. Am. Chem. Soc. 2015, vol.137, issue.13, pp.9354-9362 ,
, Biochemistry Biochemistry E, vol.9, issue.2317, pp.2715-6793, 1984.
, Proteins: Struct., Funct. J. Biomol. NMR, vol.9, issue.18, p.359, 1069.
(21) Sklenar, V. Basic Life Sci, Proteins: Struct., Funct. J. Biomol. NMR J. Biomol. NMR J. Magn. Reson. P. T, vol.2, issue.99, pp.661-63, 1990. ,
, , pp.6150-6175, 1989.
, J. Magn. Reson, vol.82, pp.163-189, 1989.
, Biochemistry Methods Mol. Biol, vol.2012, issue.5128, pp.9535-9562, 1076.
, J
, Nucleic Acids Res, vol.42, issue.6, pp.222-230, 2005.
, Nucleic Acids Res J, vol.41, pp.8-31, 2013.
, J. Mol. Biol. J. Mol. Biol, vol.376, issue.368, pp.1142-1174, 2007.
, J. Am. Chem
, Proteins: Struct., Funct., Genet, pp.449-484, 1994.
Microsecond Folding Experiments and Simulations: A Match Is Made Designing a 20-Residue Protein, Journal of the American Chemical Society Article DOI: 10.1021 3372?3388. (2) 425?430. (3) Barua, 2002. ,
The Trp-Cage: Optimizing the Stability of a Globular Miniprotein, 171?185. (4) Pitera, J. W.; Swope, W. Understanding Folding and Design: Replica-Exchange Simulations of ? ? Trp-Cage'' Miniproteins. Proc. Natl, 2008. ,
Charged Termini on the Trp-Cage Roughen the Folding Energy Landscape Computing the Stability Diagram of the Trp-Cage Miniprotein Ab Initio Folding Simulation of the Trp-Cage Mini-Protein Approaches NMR Resolution The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations Microsecond Simulations of the Folding/ Unfolding Thermodynamics of the Trp-Cage Miniprotein, 7874?7881. (6) Proc. Natl. Acad. Sci. U. S. A. 17754?17759. (7) Chowdhury, 711?717. (8) Snow 14548?14549. (9) 1889?1899. (10) Paschek, D.; Nymeyer, H.; García, A. E. Replica Exchange Simulation of Reversible Folding/unfolding of the Trp-Cage Miniprotein in Explicit Solvent: On the Structure and Possible Role of Internal Water 524?533. (11) Simmerling, C.; Strockbine, B.; Roitberg, A. E. All-Atom Structure Prediction and Folding Simulations of a Stable Protein, 2002. ,
Smaller and Faster: The 20-Residue Trp-Cage Protein Folds in 4 Ms, 11258?11259. (12), 2002. ,
, 12952?12953. (13), 2002.
Existing Hydrophobic Collapse in the Unfolded State of an Ultrafast Folding Protein, 106?109. (14), 2007. ,
Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes Simulation of the Thermodynamics of Folding and Unfolding of the Trp-Cage Mini-Protein TC5b Using Different Combinations of Force Fields and Solvation Models Sampling the Multiple Folding Mechanisms of Trp-Cage in Explicit Solvent, Atomic-Level Structure Characterization of an Ultrafast Folding Mini-Protein Denatured State 599?608. (16) 15859?15864. (18) Jimenez-Cruz, C. A.; Makhatadze, G. I, pp.41301-41316, 2006. ,
Temperature and Urea Induced Denaturation of the TRP-Cage Mini Protein TC5b: A Simulation Study Consistent with Experimental Observations Thermodynamics of the Trp-Cage Miniprotein Unfolding in Urea, Protonation/deprotonation Effects on the Stability of the Trp-Cage Miniprotein 1376?1381. (21) Kosmotropes and Chaotropes: Modelling Preferential Exclusion, Binding and Aggregate Stability 45?57. (23) Canchi, D. R.; Jayasimha, pp.17056-273, 2004. ,
Molecular Mechanism for the Preferential Exclusion of Osmolytes from Protein Surfaces Equilibrium Study of Protein Denaturation by Urea, 2338? 2344. (25) English, C. A.; García, A. E. Folding and Unfolding Thermodynamics of the TC10b Trp-Cage Miniprotein. Phys. Chem, pp.189-213 ,
A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations Revisiting Volume Changes in Pressure-Induced Protein Unfolding Exploring the Folding Energy Landscape with Pressure, 201?209. (28) 110?115. (29) Rouget, J. Size and Sequence and the Volume Change of Protein Folding 6020?6027. (30) ProteinVolume: Calculating Molecular van Der Waals and Void Volumes in Proteins. BMC Bioinf. 2015 Royer, C. A. Cavities Determine the Pressure Unfolding of Proteins. Proc. Natl, pp.2748-2774, 2002. ,
Redefining the Dry Molten Globule State of Proteins, 6945?6950. (32) 2520?2528. (33) Paschek, D.; Gnanakaran, S.; Garcia, A. E. Simulations of the Pressure and Temperature Unfolding of an Alpha-Helical Peptide, p.426, 2012. ,
Effect of pressure on helix-coil transition of an alanine-based peptide: An FTIR study, Proc. Natl. Acad. Sci. U. S. A. 2005 6765?6770. (34) 911?918. (35) Imamura Effect of Pressure on the Secondary Structure of Coiled Coil Peptide GCN4-p1, 2009. ,
DOI : 10.1016/j.bbapap.2005.06.005
Achieving Secondary Structural Resolution in Kinetic Measurements of Protein Folding: A Case Study of the Folding Mechanism of Trp-Cage Using D-Amino Acids to Delineate the Mechanism of Protein Folding: Application to Trp-Cage, 10884?10887. (37) 131?134. (38) Bunagan, M. R.; Yang, X.; Saven, J. G.; Gai, F. Ultrafast Folding of a Computationally Designed Trp-Cage Mutant: Trp 2-Cage. J. Phys, pp.193-198, 2010. ,
NMRPipe: A Multidimensional Spectral Processing System Based on UNIX Pipes A Computer Program for the Visualization and Analysis of NMR Data, 3759?3763. (39) 603?614. (41) Protein NMR Structure Determination with Automated NOE Assignment Using the New Software CANDID and the Torsion Angle Dynamics Algorithm DYANA 209?227. (42) Bru? nger, pp.277-293, 1994. ,
Crystallography & amp; NMR System: A New Software Suite for Macromolecular Structure Determination, 905?921. (43) Brunger, A. T. Version 1.2 of the Crystallography and NMR System 2728?2733. (44) Peterson, R. W.; Nucci, N. V.; Wand, A. J. Modification of Encapsulation Pressure of Reverse Micelles in Liquid Ethane. J. Magn, 1998. ,
KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies, 31?52. (46) Jorgensen, W. L.; Chandrasekhar, pp.229-233, 2007. ,
DOI : 10.1007/BF00197807
Comparison of Simple Potential Functions for Simulating Liquid Water, 926. (47) Hornak, 1983. ,
Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features 2577?2637. (49) Buckingham, A. D. Chemical Shifts in the Nuclear Magnetic Resonance Spectra of Molecules Containing Polar Groups, 712?725. (48) 300?307. (50), 1960. ,
, J. Am. Chem. Soc, vol.125, pp.9556-9557, 2003.
Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations, J ,
, 16968?16976. (52), pp.53-75, 2013.
Measuring the Strength of Side-Chain Hydrogen Bonds in Peptide Helices: The Gln.Asp (I, I + 4) Interaction, Biochemistry, vol.2454, issue.41, pp.752-761, 1995. ,
, (? 12 ? 16H) Add 1mL of 500mM IPTG, and put the solution at around 20 ? C (to avoid protein aggregation) for 12 to 16 hours. After this step is completed, spin the cells down in polycarbonate tubes (? 7000g), get rid of the excess liquid, and freeze the pellet. The production process can be interrupted here
, Protein purification Resuspend cells into 50ml buffer A, add 100µL of 10mg/mL lysozyme and 1 protease inhibitor tablet (EDTA free)
, Freeze and thaw the solution three times
, Add 1mL of 1mg/mL DNase, 100µL of M gCl 2
, Wash with 50 mL of buffer A. Elute with 50 mL of buffer B. Run gel (12-15%) using the washing liquid and check the presence of your protein in the eluting solution, Load the supernatant onto Ni2+ column
, Dialyze protein into the dialysis buffer (4 ? C)
Fractional contact maps calculated from the pseudo free energy profile at 288 K. A-F correspond to the different Q value ranges defined in the Pseudo free energy profile in Figure S7. Grey dots correspond to the original contact map, colored dots correspond to the proportion of contact found in the given contact range, color code is given by the color scale of p(i,j) ,
, Grey dashed lines represent the limits of each repeat in the protein primary sequence
Fractional contact maps calculated from the pseudo free energy profile at 298 K. A-F correspond to the different Q value ranges defined in the Pseudo free energy profile in Figure S8. Grey dots correspond to the original contact map, colored dots correspond to the proportion of contact found in the given contact range, color code is given by the color scale of p(i,j) ,
, Grey dashed lines represent the limits of each repeat in the protein primary sequence
Royer 1,c * and Christian Roumestand 1 * Supplementary Material Supplementary Figure 3 Thermal dependences of pressure induced unfolding of A) the ultrastable ?+PHS protein (grey) and the single mutants B) L125A (red) and C) I92A (green) and D) the corresponding double mutant L125/I92A (orange) as followed by 2D 15 N-1 H HSQC. First column: normalized intensity profiles of individual amides as a function of pressure. Second column: histogram of single residue ?V f values derived from two-state unfolding model fit to intensity profiles. Under equilibrium conditions, native cross-peak intensities were integrated from the corresponding HSQC spectrum and the resulting intensity versus pressure data points were individually fitted for each resonance. The fitting procedure was equivalent to the one used for the high-pressure fluorescence experiments described in Figure S4, except no correction for quantum yield was applied. Experiments were recorded, and L125/I92A respectively. Fitting ?V f errors bars are shown as thin black lines ,
, , p.202
, fluorescence (black circles) and PPC (blue circle) Red line is a quadratic fit to ?V NMR and ?V PPC data. Black line is a quadratic fit to ?V fluorescence and ?V PPC data. Grey lines are linear fits to single residue ?V NMR data. PPC experiments were carried out in 10 mM Phosphate buffer pH 5.5. Fluorescence experiments were carried out in 10 mM Bis-tris ph 5
, Proc. Natl. Acad. Sci. U. S. A, pp.6945-6950, 2012.
, Journal of Biomolecular NMR, vol.9, issue.4, pp.359-369, 1997.
DOI : 10.1023/A:1018334207887
High-Pressure Fluorescence Applications, Methods Mol. Biol, vol.1076, pp.53-74, 2014. ,
DOI : 10.1007/978-1-62703-649-8_4
Probing the Physical Determinants of Thermal Expansion of Folded Proteins, The Journal of Physical Chemistry B, vol.117, issue.42, pp.12742-12749, 2013. ,
DOI : 10.1021/jp401113p
, Nucleic Acids Res, pp.41-49, 2013.
Cold denaturation as a tool to measure protein stability, Biophysical Chemistry, vol.208, pp.4-8, 2016. ,
DOI : 10.1016/j.bpc.2015.05.007
Estimating the hydrogen bond energy. The journal of physical chemistry, A, vol.114, pp.9529-9536, 2010. ,
The Contribution of Entropy, Enthalpy, and Hydrophobic Desolvation to Cooperativity in Repeat-Protein Folding, Structure, vol.19, issue.3, pp.349-360, 2011. ,
DOI : 10.1016/j.str.2010.12.018
Designing a 20-residue protein, Nature Structural Biology, vol.9, issue.6, pp.425-430, 2002. ,
DOI : 10.1038/nsb798
Experimental measurement of the effective dielectric in the hydrophobic core of a protein, Biophysical Chemistry, vol.64, pp.1-3211, 1997. ,
Probing the Physical Determinants of Thermal Expansion of Folded Proteins, The Journal of Physical Chemistry B, vol.117, issue.42, pp.12742-12749, 2013. ,
DOI : 10.1021/jp401113p
Experimental investigation of the frequency and substitution dependence of negative ?-values in two-state proteins, Biochemistry, issue.36, pp.4412160-12167, 2005. ,
How to fold graciously, Mössbauer Spectroscopy in Biological Systems Proceedings, pp.22-24, 1969. ,
Are there pathways for protein folding? Journal de Chimie Physique et de Physico-Chimie Biologique, pp.44-45, 1968. ,
The Protein Folding Problem, Annual Review of Biophysics, vol.37, issue.1, pp.289-316, 2008. ,
DOI : 10.1146/annurev.biophys.37.092707.153558
Funnels, pathways, and the energy landscape of protein folding: A synthesis, Proteins: Structure, Function, and Genetics, vol.90, issue.3, pp.167-195, 1995. ,
DOI : 10.1146/annurev.pc.40.100189.001231
A Comparison of the pH, Urea, and Temperature-denatured States of Barnase by Heteronuclear NMR: Implications for the Initiation of Protein Folding, Journal of Molecular Biology, vol.254, issue.2, pp.305-321, 1995. ,
DOI : 10.1006/jmbi.1995.0618
Evidence for residual structure in acid-and heat-denatured proteins, Journal of Biological Chemistry, vol.242, pp.4486-4489, 1967. ,
Denatured States of Proteins, Annual Review of Biochemistry, vol.60, issue.1, pp.795-825, 1991. ,
Characterization of a partly folded protein by NMR methods: studies on the molten globule state of guinea pig .alpha.-lactalbumin, Biochemistry, vol.28, issue.1, pp.7-13, 1989. ,
DOI : 10.1021/bi00427a002
Models of Cooperativity in Protein Folding, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.348, issue.1323, pp.61-70, 1323. ,
DOI : 10.1098/rstb.1995.0046
Thermodynamics of protein denaturation. Effect of pressure on the denaturation on ribonuclease A, Biochemistry, vol.9, issue.4, pp.1038-1047, 1970. ,
Revisiting volume changes in pressure-induced protein unfolding, Biochimica et Biophysica Acta, vol.1595, issue.12, pp.201-209, 2002. ,
Moderate pressure has no distinct impact on hydrophobic hydration of proteins, Thermochimica Acta, vol.610, pp.10-15, 2015. ,
Enthalpy and entropy contributions to the pressure dependence of hydrophobic interactions, The Journal of Chemical Physics, vol.116, issue.6, p.2480, 2002. ,
DOI : 10.1016/S0006-3495(97)78647-8
Common features of protein unfolding and dissolution of hydrophobic compounds, Science, vol.247, issue.4942, pp.247559-561, 1990. ,
DOI : 10.1126/science.2300815
Heat capacity of hydrogen-bonded networks: an alternative view of protein folding thermodynamics, Biophysical Chemistry, vol.85, issue.1, pp.25-39, 2000. ,
DOI : 10.1016/S0301-4622(00)00136-8
Hydrophobic Effect, Water Structure, and Heat Capacity Changes, The Journal of Physical Chemistry B, vol.101, issue.21, pp.4343-4348, 1997. ,
DOI : 10.1021/jp9702457
Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding, Physical Review Letters, vol.48, issue.24, pp.4966-4968, 1996. ,
DOI : 10.1103/PhysRevE.48.2898
URL : http://arxiv.org/pdf/physics/9611013
Water structure changes induced by hydrophobic and polar solutes revealed by simulations and infrared spectroscopy, The Journal of Chemical Physics, vol.70, issue.4, p.1791, 2001. ,
DOI : 10.1039/C29710001404
Spin glasses and the statistical mechanics of protein folding, pp.7524-7528, 1987. ,
Optimal protein-folding codes from spin-glass theory., Proceedings of the National Academy of Sciences, vol.89, issue.11, pp.4918-4922, 1992. ,
DOI : 10.1073/pnas.89.11.4918
URL : http://www.pnas.org/content/89/11/4918.full.pdf
pH and temperatureinduced molten globule-like denatured states of equinatoxin II: A study by UV-melting, DSC, far-and near-UV CD spectroscopy, and ANS fluorescence, Biochemistry, issue.47, pp.3614345-14352, 1997. ,
DOI : 10.1021/bi971719v
Using nuclear magnetic resonance spectroscopy to study molten globule states of proteins, Methods, vol.34, issue.1, pp.121-132, 2004. ,
DOI : 10.1016/j.ymeth.2004.03.009
??-lactalbumin: compact state with fluctuating tertiary structure?, FEBS Letters, vol.253, issue.2, pp.311-315, 1981. ,
DOI : 10.1021/bi00562a003
URL : http://onlinelibrary.wiley.com/doi/10.1016/0014-5793(81)80642-4/pdf
Dry molten globule intermediates and the mechanism of protein unfolding, Proteins: Structure, Function, and Bioinformatics, vol.76, issue.13, pp.782725-2737, 2010. ,
DOI : 10.1016/0005-2795(71)90271-6
URL : http://europepmc.org/articles/pmc2927783?pdf=render
Transient intermediates in the folding of dihydrofolate reductase as detected by far-ultraviolet circular dichroism spectroscopy, Biochemistry, vol.30, issue.31, pp.307693-7703, 1991. ,
DOI : 10.1021/bi00245a005
???Molten-globule state???: a compact form of globular proteins with mobile side-chains, FEBS Letters, vol.22, issue.1, pp.21-24, 1983. ,
DOI : 10.1002/bip.360220115
URL : http://onlinelibrary.wiley.com/doi/10.1016/0014-5793(83)80010-6/pdf
Formation of a Molten Globule Intermediate Early in the Kinetic Folding Pathway of Apomyoglobin, Science, vol.262, pp.892-896, 1993. ,
Evidence for a molten globule state as a general intermediate in protein folding, FEBS Letters, vol.58, issue.1, pp.20-24, 1990. ,
DOI : 10.1016/0022-2836(71)90243-9
URL : http://onlinelibrary.wiley.com/doi/10.1016/0014-5793(90)80143-7/pdf
Direct evidence for a dry molten globule intermediate during the unfolding of a small protein, Proceedings of the National Academy of Sciences of the United States of America, pp.12289-94, 2009. ,
Study of the ?molten globule? intermediate state in protein folding by a hydrophobic fluorescent probe, Biopolymers, vol.263, issue.1, pp.31119-128, 1991. ,
DOI : 10.1042/bj1550331
Alpha-lactalbumin forms a compact molten globule in the absence of disulfide bonds, Nature Structural Biology, vol.6, issue.10, pp.948-952, 1999. ,
DOI : 10.1038/13318
Evidence for a molten globule-like transition state in protein folding from determination of activation volumes, Biochemistry, vol.34, issue.15, pp.4909-4912, 1995. ,
Denaturant-induced movement of the transition state of protein folding revealed by high-pressure stopped-flow measurements, Proceedings of the National Academy of Sciences, vol.57, issue.20, pp.17-22, 2000. ,
DOI : 10.1021/ja01305a017
Unique features of the folding landscape of a repeat protein revealed by pressure perturbation, Biophysical Journal, issue.11, pp.982712-2721, 2010. ,
Hydration of the folding transition state ensembly of a protein, Biochemistry, issue.11, pp.453473-3480, 2006. ,
Kinetics of hydrogen bond breakage in the process of unfolding of ribonuclease A measured by pulsed hydrogen exchange., Proceedings of the National Academy of Sciences, vol.92, issue.7, pp.2657-61, 1995. ,
DOI : 10.1073/pnas.92.7.2657
Formation of a Molten Globule Intermediate Early in the Kinetic Folding Pathway of Apomyoglobin, Science, vol.262, pp.892-896, 1993. ,
How fast is protein hydrophobic collapse?, Proceedings of the National Academy of Sciences, vol.11, issue.2, pp.12117-12122, 2003. ,
DOI : 10.1016/S0959-440X(00)00192-5
URL : http://europepmc.org/articles/pmc218722?pdf=render
Molecular collapse: The rate-limiting step in two-state cytochrome c folding, Proteins: Structure, Function, and Genetics, vol.34, issue.4, pp.413-426, 1996. ,
DOI : 10.1063/1.1747547
Comparison of equilibrium and kinetic approaches for determining protein folding mechanisms, Advances in Protein Chemistry, pp.283-328, 2000. ,
Funnels, pathways, and the energy landscape of protein folding: A synthesis, Proteins: Structure, Function, and Genetics, vol.90, issue.3, pp.167-95, 1995. ,
DOI : 10.1146/annurev.pc.40.100189.001231
Structural transitions during activation and ligand binding in hexadecameric Rubisco inferred from the crystal structure of the activated unliganded spinach enzyme, Nature Structural Biology, vol.3, issue.1, pp.95-101, 1996. ,
The foldon universe: a survey of structural similarity and self-recognition of independently folding units, Journal of Molecular Biology, vol.272, issue.1, pp.95-105, 1997. ,
Protein folding: The stepwise assembly of foldon units, Proceedings of the National Academy of Sciences, pp.4741-4746, 2005. ,
DOI : 10.1073/pnas.98.1.105
URL : http://www.pnas.org/content/102/13/4741.full.pdf
Hydrogen exchange methods to study protein folding, Methods, vol.34, issue.1, pp.51-64, 2004. ,
Extracting information on folding from the amino acid sequence: Accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions, Biochemistry, vol.31, issue.42, pp.3110226-10238, 1992. ,
DOI : 10.1021/bi00157a009
Contact order, transition state placement and the refolding rates of single domain proteins, Journal of Molecular Biology, vol.277, issue.4, pp.985-994, 1998. ,
Class-specific correlations between protein folding rate, structure-derived, and sequence-derived descriptors, Proteins: Structure, Function, and Bioinformatics, vol.54, issue.2, pp.333-341, 2003. ,
Extracting information on folding from the amino acid sequence: Consensus regions with preferred conformation in homologous proteins, Biochemistry, vol.31, issue.42, pp.3110239-10249, 1992. ,
DOI : 10.1021/bi00157a010
History of the Lenz-Ising Model, Reviews of Modern Physics, vol.27, issue.4, pp.883-893, 1967. ,
DOI : 10.1016/0031-8914(61)90091-X
, Protein Folding, and N Go Theoretical studies of protein folding. Annual review of biophysics and bioengineering, Theoretical Studies Of, pp.183-210, 1983.
Chapter 4 Analysis of Repeat???Protein Folding Using Nearest???Neighbor Statistical Mechanical Models, 2009. ,
DOI : 10.1016/S0076-6879(08)04204-3
Repeat-protein folding: New insights into origins of cooperativity, stability, and topology, Archives of Biochemistry and Biophysics, vol.469, issue.1, pp.83-99, 2008. ,
DOI : 10.1016/j.abb.2007.08.034
An experimentally determined protein folding energy landscape, 2004. ,
Highly polarized C-terminal transition state of the leucine-rich repeat domain of PP32 is governed by local stability, Proceedings of the National Academy of Sciences, vol.40, issue.4, pp.2298-2306, 2015. ,
DOI : 10.1002/prot.340170110
History of the Lenz-Ising Model 1920?1950: From Ferromagnetic to Cooperative Phenomena, Archive for History of Exact Sciences, vol.59, issue.3, pp.267-318, 2005. ,
DOI : 10.1007/s00407-004-0088-3
Structure and stability of designed TPR protein superhelices: unusual crystal packing and implications for natural TPR proteins, Acta Crystallographica Section D Biological Crystallography, vol.63, issue.7 ,
DOI : 10.1107/S0907444907024353
, Acta Crystallographica Section D: Biological Crystallography, vol.63, issue.7, pp.800-811, 2007.
Direct Observation of Parallel Folding Pathways Revealed Using a Symmetric Repeat Protein System, Biophysical Journal, vol.107, issue.1, pp.220-252, 2014. ,
DOI : 10.1016/j.bpj.2014.04.058
Is there a unifying mechanism for protein folding?, Trends in Biochemical Sciences, vol.28, issue.1, pp.18-25, 2003. ,
DOI : 10.1016/S0968-0004(02)00012-9
Limited cooperativity in protein folding, Current Opinion in Structural Biology, vol.36, pp.58-66, 2016. ,
DOI : 10.1016/j.sbi.2015.12.001
A to Z of Thermodynamics, 1998. ,
Stability of troponin C, BBA) -Protein Structure, pp.196-204, 1980. ,
Temperature dependence of the hydrophobic interaction in protein folding, Proceedings of the National Academy of Sciences, pp.8069-8072, 1986. ,
On the entropy of protein folding, Protein Science, vol.5, issue.3, pp.507-510, 1996. ,
On the origin of the enthalpy and entropy convergence temperatures in protein folding., Proceedings of the National Academy of Sciences, pp.9335-9338, 1992. ,
DOI : 10.1073/pnas.89.19.9335
Group additivity thermodynamics for dissolution of solid cyclic dipeptides into water, Thermochimica Acta, vol.172, pp.11-20, 1990. ,
DOI : 10.1016/0040-6031(90)80555-D
Solid model compounds and the thermodynamics of protein unfolding, Journal of Molecular Biology, vol.222, issue.3, pp.699-709, 1991. ,
Contribution of Hydration to Protein Folding Thermodynamics, Journal of Molecular Biology, vol.232, issue.2, pp.660-679, 1993. ,
Hydration effects in protein unfolding, Biophysical Chemistry, vol.51, issue.2-3, pp.291-309, 1994. ,
The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding, Proceedings of the National Academy of Sciences of the United States of America, pp.12565-70, 2000. ,
DOI : 10.1002/pro.5560030317
URL : http://www.pnas.org/content/97/23/12565.full.pdf
Side-chain conformational entropy in protein folding Protein science : a publication of the, pp.2247-2251, 1995. ,
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations, Proceedings of the National Academy of Sciences of the United States of America, issue.43, pp.11115396-401, 2014. ,
The role of conformational entropy in molecular recognition by calmodulin, Nature Chemical Biology, vol.50, issue.5, pp.352-358, 2010. ,
DOI : 10.1002/prot.1
Microscopic Insights into the NMR Relaxation-Based Protein Conformational Entropy Meter, Journal of the American Chemical Society, vol.135, issue.40, pp.15092-15100, 2013. ,
DOI : 10.1021/ja405200u
URL : http://europepmc.org/articles/pmc3821934?pdf=render
Estimating entropies from molecular dynamics simulations, The Journal of Chemical Physics, vol.9, issue.6, pp.2652-2661, 2004. ,
DOI : 10.1063/1.447824
URL : http://dare.ubvu.vu.nl/bitstream/1871/22115/2/233938.pdf
Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding Protein science : a publication of the, pp.2138-2186, 1995. ,
Heat capacity changes upon burial of polar and nonpolar groups in proteins, pp.1343-1352, 2001. ,
Protein Heat Capacity: An Anomaly that Maybe Never Was, The Journal of Physical Chemistry Letters, vol.1, issue.22, pp.3298-3304, 2010. ,
DOI : 10.1021/jz1012142
Heat capacity and compactness of denatured proteins, Biophysical Chemistry, vol.78, issue.1-2, pp.207-217, 1999. ,
DOI : 10.1016/S0301-4622(99)00022-8
URL : http://www.sci.ccny.cuny.edu/~themis/heat.pdf
Role of Hydrophobic Hydration in Protein Stability: A 3D Water-Explicit Protein Model Exhibiting Cold and Heat Denaturation, The Journal of Physical Chemistry B, vol.116, issue.28, pp.8095-8104, 2012. ,
DOI : 10.1021/jp3039175
ProteinVolume: calculating molecular van der Waals and void volumes in proteins, BMC bioinformatics, vol.16, issue.1, p.101, 2015. ,
Volume, expansivity and isothermal compressibility changes associated with temperature and pressure unfolding of staphylococcal nuclease 1 1Edited by C. R. Mathews, Journal of Molecular Biology, vol.307, issue.4, pp.1091-1102, 2001. ,
DOI : 10.1006/jmbi.2001.4517
Protein volumes and hydration effects. The calculations of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences, European Journal of Biochemistry, vol.157, issue.1, pp.169-180, 1986. ,
Interfaces and the driving force of hydrophobic assembly, Nature, vol.10, issue.7059, pp.640-647, 2005. ,
DOI : 10.1007/978-1-4684-3545-0
Size and Sequence and the Volume Change of Protein Folding, Journal of the American Chemical Society, vol.133, issue.15, pp.6020-6027, 2011. ,
DOI : 10.1021/ja200228w
URL : http://europepmc.org/articles/pmc3151578?pdf=render
Applications of pressure perturbation calorimetry to study factors contributing to the volume changes upon protein unfolding, BBA) -General Subjects, pp.18601036-1042, 2016. ,
Cavities determine the pressure unfolding of proteins, Proceedings of the National Academy of Sciences, pp.6945-6950, 2012. ,
DOI : 10.1529/biophysj.106.090266
URL : http://www.pnas.org/content/109/18/6945.full.pdf
Effect of Internal Cavities on Folding Rates and Routes Revealed by Real-Time Pressure-Jump NMR Spectroscopy, Journal of the American Chemical Society, vol.135, issue.39, pp.13514610-14618, 2013. ,
DOI : 10.1021/ja406682e
Structural, energetic, and dynamic responses of the native state ensemble of staphylococcal nuclease to cavity-creating mutations, Proteins: Structure, Function, and Bioinformatics, vol.250, issue.6, pp.811069-1080, 2013. ,
DOI : 10.1006/jmbi.1995.0365
Exploring volume, compressibility and hydration changes of folded proteins upon compression, Phys. Chem. Chem. Phys, p.2015 ,
Calculation of the volumetric characteristics of biomacromolecules in solution by the Voronoi-Delaunay technique, Biophysical Chemistry, vol.192, pp.1-9, 2014. ,
Determination of the volumetric properties of proteins and other solutes using pressure perturbation calorimetry, Analytical biochemistry, vol.302, issue.1, pp.144-60, 2002. ,
Protein hydration and volumetric properties, Current Opinion in Colloid & Interface Science, vol.16, issue.6, pp.568-571, 2011. ,
DOI : 10.1016/j.cocis.2011.04.008
, Biochemistry, vol.38, issue.13, pp.4157-4164, 1999.
DOI : 10.1021/bi982608e
Pressure Perturbation Calorimetic Studies of the Solvation Properties and the Thermal Unfolding of Proteins in Solution, Zeitschrift für Physikalische Chemie, pp.10-20031221, 2003. ,
DOI : 10.1021/ja00995a002
Towards a Quantitative Understanding of Protein Hydration and Volumetric Properties, ChemPhysChem, vol.82, issue.18, pp.2715-2721, 2008. ,
DOI : 10.1016/S0006-3495(02)75670-1
Disentangling Volumetric and Hydrational Properties of Proteins, The Journal of Physical Chemistry B, vol.119, issue.5, pp.1881-1890, 2015. ,
On the Molecular Origins of Volumetric Data, The Journal of Physical Chemistry B, vol.112, issue.3, pp.911-917, 2008. ,
Evolutionarily Conserved Pattern of Interactions in a Protein Revealed by Local Thermal Expansion Properties, Journal of the American Chemical Society, vol.137, issue.29, pp.1379354-9362, 2015. ,
DOI : 10.1021/jacs.5b04320
URL : https://hal.archives-ouvertes.fr/hal-01276620
Pressure Perturbation Calorimetry of Unfolded Proteins, The Journal of Physical Chemistry B, vol.114, issue.49, pp.16166-16170, 2010. ,
[14]Determination and analysis of urea and guanidine hydrochloride denaturation curves, Methods in enzymology, vol.131, pp.266-280, 1986. ,
DOI : 10.1016/0076-6879(86)31045-0
Thermodynamics of Protein Interactions with Urea and Guanidinium Hydrochloride, The Journal of Physical Chemistry B, vol.103, issue.23, pp.4781-4785, 1999. ,
DOI : 10.1021/jp990413q
Linear extrapolation method of analyzing solvent denaturation curves, Proteins: Structure, Function, and Genetics, vol.28, issue.S4, pp.1-7, 2000. ,
DOI : 10.1515/bchm2.1900.30.1-2.182
Impact of urea on water structure: a clue to its properties as a denaturant?, Biophysical Chemistry, vol.105, issue.2-3, pp.649-666, 2003. ,
DOI : 10.1016/S0301-4622(03)00095-4
Impact of Protein Denaturants and Stabilizers on Water Structure, Journal of the American Chemical Society, vol.126, issue.7, pp.1958-1961, 2004. ,
DOI : 10.1021/ja039335h
Properties of urea-water solvation calculated from a new ab initio polarizable intermolecular potential, The Journal of Chemical Physics, issue.11, p.958419, 1991. ,
Effect of urea on the structural dynamics of water, Proceedings of the National Academy of Sciences, pp.18417-18420, 2006. ,
DOI : 10.1071/CH9672087
Preferential Solvation in Urea Solutions at Different Concentrations:?? Properties from Simulation Studies, The Journal of Physical Chemistry B, vol.111, issue.19, pp.5233-5242, 2007. ,
DOI : 10.1021/jp067659x
URL : http://europepmc.org/articles/pmc2583237?pdf=render
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding, Proceedings of the National Academy of Sciences, pp.16928-16933, 2008. ,
DOI : 10.1063/1.472061
URL : http://www.pnas.org/content/105/44/16928.full.pdf
Protein denaturation by urea: Slash and bond, Proceedings of the National Academy of Sciences, vol.105, issue.44, pp.16825-16826, 2008. ,
Equilibrium study of protein denaturation by urea, Journal of the American Chemical Society, vol.132, issue.7, pp.2338-2344, 2010. ,
Backbone and side-chain contributions in protein denaturation by urea, Biophysical Journal, vol.100, issue.6, pp.1526-1533, 2011. ,
Prokaryotes, American Scientist, vol.87, issue.6, pp.518-525, 2016. ,
DOI : 10.1511/1999.42.837
Macromolecular crowding: obvious but underappreciated, Trends in Biochemical Sciences, vol.26, issue.10, pp.597-604, 2001. ,
DOI : 10.1016/S0968-0004(01)01938-7
In-cell thermodynamics and a new role for protein surfaces, Proceedings of the National Academy of Sciences, 2016. ,
DOI : 10.1371/journal.pone.0072286
Role of naturally occurring osmolytes in protein folding and stability, Archives of Biochemistry and Biophysics, vol.491, issue.1-2, pp.1-6, 2009. ,
DOI : 10.1016/j.abb.2009.09.007
Cosolvent Effects on Protein Stability, Annu. Rev. Phys. Chem, vol.64, pp.273-93, 2013. ,
Structure and Energetics of the Hydrogen-Bonded Backbone in Protein Folding, Annual Review of Biochemistry, vol.77, issue.1, pp.339-362, 2008. ,
DOI : 10.1146/annurev.biochem.77.061306.131357
Protein Stabilization by Macromolecular Crowding through Enthalpy Rather Than Entropy, Journal of the American Chemical Society, vol.136, issue.25, pp.9036-9041, 2014. ,
DOI : 10.1021/ja503205y
Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences, Annual Review of Biophysics, vol.37, issue.1, pp.375-397, 2008. ,
DOI : 10.1146/annurev.biophys.37.032807.125817
URL : http://europepmc.org/articles/pmc2826134?pdf=render
Dielectric constant of ionic solutions: A field-theory approach. Physical review letters, 2012. ,
DOI : 10.1103/physrevlett.108.227801
URL : http://arxiv.org/pdf/1201.6081
Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect, Science, vol.255, issue.5041, pp.255178-183, 1992. ,
DOI : 10.1126/science.1553543
Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease, Biochemistry, vol.29, issue.35, pp.298033-8041, 1990. ,
DOI : 10.1021/bi00487a007
Capping motifs stabilize the leucine-rich repeat protein PP32 and rigidify adjacent repeats, Protein Science, vol.23, issue.6, pp.801-811, 2014. ,
Reversible pressure-temperature denaturation of chymotrypsinogen, Biochemistry, vol.10, issue.13, pp.2436-2442, 1971. ,
DOI : 10.1021/bi00789a002
Structural characterization of the pressure-denatured state and unfolding/refolding kinetics of staphylococcal nuclease by synchrotron small-angle X-ray scattering and Fourier-transform infrared spectroscopy 1 1Edited by P. E. Wright, Journal of Molecular Biology, vol.275, issue.2, pp.389-402, 1998. ,
DOI : 10.1006/jmbi.1997.1454
Thermodynamic study of the apomyoglobin structure, Journal of Molecular Biology, vol.202, issue.1, pp.127-138, 1988. ,
DOI : 10.1016/0022-2836(88)90525-6
On the Temperature-Pressure Free-Energy Landscape of Proteins, ChemPhysChem, vol.3, issue.4, pp.359-365, 2003. ,
DOI : 10.1039/b100246p
Pressure???temperature phase diagrams of biomolecules, Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, vol.1595, issue.1-2, pp.11-29, 2002. ,
DOI : 10.1016/S0167-4838(01)00332-6
, Fundamentals of Protein NMR Spectroscopy Focus on Structural Biology, vol.5, 2006.
, Teodor Parella. NMR Periodic Table, 2000.
Unified theory of exchange effects on nuclear magnetic resonance line shapes, Journal of the American Chemical Society, vol.91, issue.6, pp.1304-1309, 1969. ,
DOI : 10.1021/ja01034a007
Two-Dimensional NMR Lineshape Analysis, Scientific Reports, vol.6, issue.1, p.24826, 2016. ,
DOI : 10.1007/BF00211777
Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB inter-union task group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy, European Journal of Biochemistry, vol.256, issue.1, pp.1-15, 1998. ,
DOI : 10.1046/j.1432-1327.1998.2560001.x
Effect of Pressure on Individual Hydrogen Bonds in Proteins, Basic Pancreatic Trypsin Inhibitor. Biochemistry, vol.37, issue.5, pp.1167-1173, 1998. ,
Pressure-induced chemical shifts as probes for conformational fluctuations in proteins, Progress in Nuclear Magnetic Resonance Spectroscopy, vol.71, pp.35-58, 2013. ,
DOI : 10.1016/j.pnmrs.2012.12.001
LINCS: A linear constraint solver for molecular simulations, Journal of Computational Chemistry, vol.19, issue.12, pp.1463-1472, 1997. ,
DOI : 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
Introduction to Molecular Dynamics with GROMACS Molecular Modeling Course 2007 Simulation of Lysozyme in Water, 2007. ,
Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes, Biophysical Journal, vol.97, issue.2, pp.599-608, 2009. ,
DOI : 10.1016/j.bpj.2009.04.061
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew, The Journal of Chemical Physics, vol.120, issue.20, p.9665, 2004. ,
DOI : 10.1016/0301-0104(89)80166-1
Molecular Dynamics: from basic techniques to applications (A Molecular Dynamics Primer), AIP Conference Proceedings, pp.95-123, 2008. ,
DOI : 10.1063/1.3040265
Molecular dynamics with coupling to an external bath, The Journal of Chemical Physics, vol.15, issue.8, pp.813684-3690, 1984. ,
DOI : 10.1039/fs9821700055
A unified formulation of the constant temperature molecular dynamics methods, The Journal of Chemical Physics, vol.81, issue.1, p.511, 1984. ,
DOI : 10.1080/00268978400100801
Canonical dynamics: Equilibrium phase-space distributions, Physical Review A, vol.31, issue.3, pp.1695-1697, 1985. ,
The Nose-Hoover thermostat, Journal of Chemical Physics, vol.83, issue.8, pp.4069-4074, 1985. ,
,
, , 2014.
Replica-exchange molecular dynamics method for protein folding, Chemical Physics Letters, vol.314, issue.1-2, pp.141-151, 1999. ,
DOI : 10.1016/S0009-2614(99)01123-9
Parallel tempering algorithm for conformational studies of biological molecules, Chemical Physics Letters, vol.281, issue.1-3, pp.140-150, 1997. ,
New Monte Carlo algorithms for protein folding, Current Opinion in Structural Biology, vol.9, issue.2, pp.177-183, 1999. ,
Exchange frequency in replica exchange molecular dynamics, The Journal of Chemical Physics, vol.2, issue.2, 2008. ,
DOI : 10.1073/pnas.0703700104
Replica-exchange Monte Carlo method for the isobaric???isothermal ensemble, Chemical Physics Letters, vol.335, issue.5-6, pp.5-6435, 2001. ,
DOI : 10.1016/S0009-2614(01)00055-0
Comparison of simple potential functions for simulating liquid water, The Journal of Chemical Physics, vol.79, issue.2, p.926, 1983. ,
DOI : 10.1016/0009-2614(80)85344-9
Comparison of multiple Amber force fields and development of improved protein backbone parameters, Proteins: Structure, Function, and Bioinformatics, vol.43, issue.3, pp.712-725, 2006. ,
DOI : 10.1002/prot.21123
Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein, Proteins: Structure, Function, and Bioinformatics, vol.101, issue.8, pp.1889-1899, 2010. ,
DOI : 10.1016/S0167-4838(01)00332-6
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures, BMC Structural Biology, vol.8, issue.1, p.49, 2008. ,
The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function, The Journal of Physical Chemistry B, vol.116, issue.29, pp.8692-8702, 2012. ,
DOI : 10.1021/jp300852d
SMOG 2: A Versatile Software Package for Generating Structure-Based Models, PLOS Computational Biology, vol.5, issue.3, pp.1-14, 2016. ,
DOI : 10.1371/journal.pcbi.1004794.t001
Fast procedure for reconstruction of full-atom protein models from reduced representations, Journal of Computational Chemistry, vol.3, issue.9, pp.1460-1465, 2008. ,
DOI : 10.1002/1097-0134(20001001)41:1<86::AID-PROT110>3.0.CO;2-Y
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol.33, issue.12, pp.2577-2637, 1983. ,
DOI : 10.1016/0005-2795(73)90350-4
,
Pressure perturbation calorimetric studies of the solvation properties and the thermal unfolding of proteins in solution experiments and theoretical interpretation. Physical chemistry chemical physics, pp.1249-65, 2006. ,
Pressure Perturbation Calorimetry ( PPC ) DSC Application Note Solvation Effects ,
The crystal structure of the tumor suppressor protein pp32 (Anp32a): Structural insights into Anp32 family of proteins, Protein Science, vol.374, issue.7, pp.1308-1315, 2007. ,
DOI : 10.1515/bchm3.1994.375.2.113
Temperature dependence of 1 H chemical shifts in proteins, Journal of Biomolecular NMR, vol.9, issue.4, pp.359-369, 1997. ,
All-Atom Structure Prediction and Folding Simulations of a Stable Protein, Journal of the American Chemical Society, vol.124, issue.38, pp.11258-11259, 2002. ,
DOI : 10.1021/ja0273851
Molecular Mechanism for the Preferential Exclusion of Osmolytes from Protein Surfaces, Biophysical Journal, vol.104, issue.2, p.189, 2013. ,
Charged Termini on the Trp-Cage Roughen the Folding Energy Landscape, The Journal of Physical Chemistry B, vol.119, issue.25, pp.7874-7881, 2015. ,
Computing the stability diagram of the Trp-cage miniprotein, Proceedings of the National Academy of Sciences, pp.17754-17759, 2008. ,
DOI : 10.1002/bip.360221211
Folding and unfolding thermodynamics of the TC10b Trp-cage miniprotein, Physical Chemistry Chemical Physics, vol.16, issue.7, p.2748, 2014. ,
Probing Conformational Fluctuation of Proteins by Pressure Perturbation, Chemical Reviews, vol.106, issue.5, pp.1814-1835, 2006. ,
DOI : 10.1021/cr040440z
Chemical shifts in biomolecules, Current Opinion in Structural Biology, vol.23, issue.2, pp.172-179, 2013. ,
DOI : 10.1016/j.sbi.2013.01.007
Hydrogen bond length and proton NMR chemical shifts in proteins, Journal of the American Chemical Society, vol.105, issue.18, pp.5948-5949, 1983. ,
DOI : 10.1021/ja00356a056
Protein interactions. Chapman and Hall, 1992. ,
Chemical reaction equilibrium analysis: theory and algorithms, 1982. ,