1
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Maity H, Nguyen HT, Hori N, Thirumalai D. Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences. J Phys Chem Lett 2024; 15:3820-3827. [PMID: 38557079 DOI: 10.1021/acs.jpclett.3c03553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Repeat RNA sequences self-associate to form condensates. Simulations of a coarse-grained single-interaction site model for (CAG)n (n = 30 and 31) show that the salt-dependent free energy gap, ΔGS, between the ground (perfect hairpin) and the excited state (slipped hairpin (SH) with one CAG overhang) of the monomer for (n even) is the primary factor that determines the rates and yield of self-assembly. For odd n, the free energy (GS) of the ground state, which is an SH, is used to predict the self-association kinetics. As the monovalent salt concentration, CS, increases, ΔGS and GS increase, which decreases the rates of dimer formation. In contrast, ΔGS for shuffled sequences, with the same length and sequence composition as (CAG)31, is larger, which suppresses their propensities to aggregate. Although demonstrated explicitly for (CAG) polymers, the finding of inverse correlation between the free energy gap and RNA aggregation is general.
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Affiliation(s)
- Hiranmay Maity
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung T Nguyen
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Naoto Hori
- School of Pharmacy, University of Nottingham, Nottingham NG72RD, United Kingdom
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, United States
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2
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Maity H, Nguyen HT, Hori N, Thirumalai D. Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation. Proc Natl Acad Sci U S A 2023; 120:e2301409120. [PMID: 37276412 PMCID: PMC10268303 DOI: 10.1073/pnas.2301409120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/10/2023] [Indexed: 06/07/2023] Open
Abstract
Low-complexity nucleotide repeat sequences, which are implicated in several neurological disorders, undergo liquid-liquid phase separation (LLPS) provided the number of repeat units, n, exceeds a critical value. Here, we establish a link between the folding landscapes of the monomers of trinucleotide repeats and their propensity to self-associate. Simulations using a coarse-grained Self-Organized Polymer (SOP) model for (CAG)n repeats in monovalent salt solutions reproduce experimentally measured melting temperatures, which are available only for small n. By extending the simulations to large n, we show that the free-energy gap, ΔGS, between the ground state (GS) and slipped hairpin (SH) states is a predictor of aggregation propensity. The GS for even n is a perfect hairpin (PH), whereas it is a SH when n is odd. The value of ΔGS (zero for odd n) is larger for even n than for odd n. As a result, the rate of dimer formation is slower in (CAG)30 relative to (CAG)31, thus linking ΔGS to RNA-RNA association. The yield of the dimer decreases dramatically, compared to the wild type, in mutant sequences in which the population of the SH decreases substantially. Association between RNA chains is preceded by a transition to the SH even if the GS is a PH. The finding that the excitation spectrum-which depends on the exact sequence, n, and ionic conditions-is a predictor of self-association should also hold for other RNAs (mRNA for example) that undergo LLPS.
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Affiliation(s)
- Hiranmay Maity
- Department of Chemistry, The University of Texas at Austin, AustinTX78712
| | - Hung T. Nguyen
- Department of Chemistry, The University of Texas at Austin, AustinTX78712
| | - Naoto Hori
- School of Pharmacy, University of Nottingham, NG7 2rD, United Kingdom
| | - D. Thirumalai
- Department of Chemistry, The University of Texas at Austin, AustinTX78712
- Department of Physics, The University of Texas at Austin, AustinTX78712
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3
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Liu Z, Thirumalai D. Residue-Dependent Transition Temperatures and Denaturant Midpoints in the Folding of a Multidomain Protein. J Phys Chem B 2022; 126:10684-10688. [PMID: 36512486 DOI: 10.1021/acs.jpcb.2c07093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As a consequence of the finite size of globular proteins, it is expected that there should be dispersions in the global melting temperature (Tm) and the denaturation midpoint (Cm). Thermodynamic considerations dictate that the dispersions, ΔTm in Tm, and ΔCm in Cm, should decrease with N, the number of residues in the protein. We performed coarse-grained simulations of the self-organized polymer (SOP) model of the multidomain protein adenylate kinase (ADK) with N = 214 in order to calculate thermal and denaturation unfolding titration curves. The results show that ΔTm/Tm and ΔCm/Cm are nonzero and follow the previously established ( Phys. Rev. Lett. 2004, 93, 268107) thermodynamic 1/N scaling for proteins accurately. For ADK, the dispersions are small (≈0.004), which implies that the melting temperature is more or less unique, which is unlike in BBL (N = 40) where ΔTm/Tm ≈ 0.03.
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Affiliation(s)
- Zhenxing Liu
- Department of Physics, Beijing Normal University, Beijing 100875, China
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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4
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Liu Z, Thirumalai D. Cooperativity and Folding Kinetics in a Multidomain Protein with Interwoven Chain Topology. ACS CENTRAL SCIENCE 2022; 8:763-774. [PMID: 35756371 PMCID: PMC9228575 DOI: 10.1021/acscentsci.2c00140] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Indexed: 06/15/2023]
Abstract
Although a large percentage of eukaryotic proteomes consist of proteins with multiple domains, not much is known about their assembly mechanism, especially those with intricate native state architectures. Some have a complex topology in which the structural elements along the sequence are interwoven in such a manner that the domains cannot be separated by cutting at any location along the sequence. Such proteins are multiply connected multidomain proteins (MMPs) with the three-domain (NMP, LID, and CORE) phosphotransferase enzyme adenylate kinase (ADK) being an example. We devised a coarse-grained model to simulate ADK folding initiated by changing either the temperature or guanidinium chloride (GdmCl) concentration. The simulations reproduce the experimentally measured melting temperatures (associated with two equilibrium transitions), FRET efficiency as a function of GdmCl concentration, and the folding times quantitatively. Although the NMP domain orders independently, cooperative interactions between the LID and the CORE domains are required for complete assembly of the enzyme. Kinetic simulations show that, on the collapse time scale, multiple interconnected metastable states are populated, attesting to the folding heterogeneity. The network of kinetically connected states reveals that the CORE domain folds only after the NMP and LID domains, reflecting the interwoven nature of the chain topology.
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Affiliation(s)
- Zhenxing Liu
- Department
of Physics, Beijing Normal University, Beijing 100875, China
| | - D. Thirumalai
- Department
of Chemistry, The University of Texas at
Austin, Austin, Texas 78712, United
States
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5
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Qin M, Denesyuk N, Liu Z, Wang W, Thirumalai D. Temperature and Guanidine Hydrochloride Effects on the Folding Thermodynamics of WW Domain and Variants. J Phys Chem B 2021; 125:11386-11391. [PMID: 34612657 DOI: 10.1021/acs.jpcb.1c06340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We used simulations based on an all-atom Go model to calculate the folding temperatures (Tfs) and free energies (ΔGs) of two variants of the WW domain, which is a small all-β-sheet protein. The results, without adjusting any parameter, are in good agreement with experiments, thus validating the simulations. We then used the molecular transfer model to predict the changes in the ΔGs and Tfs as the guanidine hydrochloride concentration is varied. The predictions can be readily tested in experiments.
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Affiliation(s)
- Meng Qin
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States.,National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, and Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, China
| | - Natalia Denesyuk
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhenxing Liu
- Department of Physics, Beijing Normal University, Beijing 100875, China
| | - Wei Wang
- School of Physics, Nanjing University, Nanjing 210093, China
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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6
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Khuri RR, Phan TV, Austin RH. Protein dynamics implications of the low- and high-temperature denaturation of myoglobin. Phys Rev E 2021; 104:034414. [PMID: 34654144 DOI: 10.1103/physreve.104.034414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 08/19/2021] [Indexed: 11/07/2022]
Abstract
We reinvestigate a simple model used in the literature concerning the thermodynamic analysis of protein cold denaturation. We derive an exact thermodynamic expression for cold denaturation and give a better approximation than exists in the literature for predicting cold denaturation temperatures in the two-state model. We discuss the "dark-side" implications of this work for previous temperature-dependent protein dynamics experiments and discuss microfluidic experimental technologies, which could explore the thermal stability range of proteins below the bulk freezing point of water.
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Affiliation(s)
- Ramzi R Khuri
- Department of Natural Sciences, Baruch College, City University of New York, New York, New York 10010, USA
| | - Trung V Phan
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - Robert H Austin
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
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7
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Nassar R, Dignon GL, Razban RM, Dill KA. The Protein Folding Problem: The Role of Theory. J Mol Biol 2021; 433:167126. [PMID: 34224747 PMCID: PMC8547331 DOI: 10.1016/j.jmb.2021.167126] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 06/26/2021] [Indexed: 10/20/2022]
Abstract
The protein folding problem was first articulated as question of how order arose from disorder in proteins: How did the various native structures of proteins arise from interatomic driving forces encoded within their amino acid sequences, and how did they fold so fast? These matters have now been largely resolved by theory and statistical mechanics combined with experiments. There are general principles. Chain randomness is overcome by solvation-based codes. And in the needle-in-a-haystack metaphor, native states are found efficiently because protein haystacks (conformational ensembles) are funnel-shaped. Order-disorder theory has now grown to encompass a large swath of protein physical science across biology.
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Affiliation(s)
- Roy Nassar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Gregory L Dignon
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Rostam M Razban
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA; Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, USA.
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8
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The Finite Size Effects and Two-State Paradigm of Protein Folding. Int J Mol Sci 2021; 22:ijms22042184. [PMID: 33671738 PMCID: PMC7926810 DOI: 10.3390/ijms22042184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/19/2022] Open
Abstract
The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size extends the transition interval of the coil-globule phase transition. Based on the pedantic derivation of the two-state model, we introduce the number of amino acid residues of a polypeptide chain as a parameter in the expressions for two cooperativity measures and reveal their physical significance. We conclude that the k2 measure, defined as the ratio of van ’t Hoff and calorimetric enthalpy is related to the degeneracy of the denatured state and describes the number of cooperative units involved in the transition; additionally, it is found that the widely discussed k2=1 is just the necessary condition to classify the protein as the two-state folder. We also find that Ωc, a quantity not limited from above and growing with system size, is simply proportional to the square of the transition interval. This fact allows us to perform the classical size scaling analysis of the coil-globule phase transition. Moreover, these two measures are shown to describe different characteristics of protein folding.
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9
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Gasic AG, Boob MM, Prigozhin MB, Homouz D, Wirth AJ, Daugherty CM, Gruebele M, Cheung MS. Critical phenomena in the temperature-pressure-crowding phase diagram of a protein. PHYSICAL REVIEW. X 2019; 9:041035. [PMID: 32642303 PMCID: PMC7343146 DOI: 10.1103/physrevx.9.041035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to maintain structural integrity. These apparently conflicting behaviors are exhibited by systems near a critical point, where distinct phases merge-a concept beyond previous studies indicating proteins have a well-defined folded/unfolded phase boundary in the pressure-temperature plane. Here, by modeling the protein phosphoglycerate kinase (PGK) on the temperature (T), pressure (P), and crowding volume-fraction (ϕ) phase diagram, we demonstrate a critical transition where phases merge, and PGK exhibits large structural fluctuations. Above the critical point, the difference between the intermediate and unfolded phases disappears. When ϕ increases, the critical point moves to lower T c. We verify the calculations with experiments mapping the T-P-ϕ space, which likewise reveal a critical point at 305 K and 170 MPa that moves to lower T c as ϕ increases. Crowding places PGK near a critical line in its natural parameter space, where large conformational changes can occur without costly free energy barriers. Specific structures are proposed for each phase based on simulation.
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Affiliation(s)
- Andrei G. Gasic
- University of Houston, Department of Physics, Houston, Texas, 77204, United States
- Center for Theoretical Biological Physics, Rice University, 77005, United States
| | - Mayank M. Boob
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
| | - Maxim B. Prigozhin
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, United States
| | - Dirar Homouz
- University of Houston, Department of Physics, Houston, Texas, 77204, United States
- Center for Theoretical Biological Physics, Rice University, 77005, United States
- Khalifa University of Science and Technology, Department of Physics, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Anna Jean Wirth
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, United States
| | - Caleb M. Daugherty
- University of Houston, Department of Physics, Houston, Texas, 77204, United States
- Center for Theoretical Biological Physics, Rice University, 77005, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, United States
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, United States
| | - Margaret S. Cheung
- University of Houston, Department of Physics, Houston, Texas, 77204, United States
- Center for Theoretical Biological Physics, Rice University, 77005, United States
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10
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Thirumalai D, Samanta HS, Maity H, Reddy G. Universal Nature of Collapsibility in the Context of Protein Folding and Evolution. Trends Biochem Sci 2019; 44:675-687. [DOI: 10.1016/j.tibs.2019.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 12/21/2022]
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11
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Dubey V, Daschakraborty S. Influence of glycerol on the cooling effect of pair hydrophobicity in water: relevance to proteins’ stabilization at low temperature. Phys Chem Chem Phys 2019; 21:800-812. [DOI: 10.1039/c8cp06513f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Glycerol reduces the cooling effect of pair hydrophobicity (reduction of hydrophobicity with decreasing temperature) in water.
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Affiliation(s)
- Vikas Dubey
- Department of Chemistry
- Indian Institute of Technology Patna
- Bihar 801106
- India
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12
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Holehouse AS, Pappu RV. Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions. Annu Rev Biophys 2018; 47:19-39. [PMID: 29345991 PMCID: PMC10740066 DOI: 10.1146/annurev-biophys-070317-032838] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proteins can collapse into compact globules or form expanded, solvent-accessible, coil-like conformations. Additionally, they can fold into well-defined three-dimensional structures or remain partially or entirely disordered. Recent discoveries have shown that the tendency for proteins to collapse or remain expanded is not intrinsically coupled to their ability to fold. These observations suggest that proteins do not have to form compact globules in aqueous solutions. They can be intrinsically disordered, collapsed, or expanded, and even form well-folded, elongated structures. This ability to decouple collapse from folding is determined by the sequence details of proteins. In this review, we highlight insights gleaned from studies over the past decade. Using a polymer physics framework, we explain how the interplay among sidechains, backbone units, and solvent determines the driving forces for collapsed versus expanded states in aqueous solvents.
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Affiliation(s)
- Alex S Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA; ,
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA; ,
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13
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Maity H, Reddy G. Thermodynamics and Kinetics of Single-Chain Monellin Folding with Structural Insights into Specific Collapse in the Denatured State Ensemble. J Mol Biol 2018; 430:465-478. [DOI: 10.1016/j.jmb.2017.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/28/2017] [Accepted: 09/09/2017] [Indexed: 01/21/2023]
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14
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Samanta HS, Zhuravlev PI, Hinczewski M, Hori N, Chakrabarti S, Thirumalai D. Protein collapse is encoded in the folded state architecture. SOFT MATTER 2017; 13:3622-3638. [PMID: 28447708 DOI: 10.1039/c7sm00074j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Folded states of single domain globular proteins are compact with high packing density. The radius of gyration, Rg, of both the folded and unfolded states increase as Nν where N is the number of amino acids in the protein. The values of the Flory exponent ν are, respectively, ≈⅓ and ≈0.6 in the folded and unfolded states, coinciding with those for homopolymers. However, the extent of compaction of the unfolded state of a protein under low denaturant concentration (collapsibility), conditions favoring the formation of the folded state, is unknown. We develop a theory that uses the contact map of proteins as input to quantitatively assess collapsibility of proteins. Although collapsibility is universal, the propensity to be compact depends on the protein architecture. Application of the theory to over two thousand proteins shows that collapsibility depends not only on N but also on the contact map reflecting the native structure. A major prediction of the theory is that β-sheet proteins are far more collapsible than structures dominated by α-helices. The theory and the accompanying simulations, validating the theoretical predictions, provide insights into the differing conclusions reached using different experimental probes assessing the extent of compaction of proteins. By calculating the criterion for collapsibility as a function of protein length we provide quantitative insights into the reasons why single domain proteins are small and the physical reasons for the origin of multi-domain proteins. Collapsibility of non-coding RNA molecules is similar β-sheet proteins structures adding support to "Compactness Selection Hypothesis".
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Affiliation(s)
- Himadri S Samanta
- Department of Chemistry, University of Texas at Austin, TX 78712, USA.
| | - Pavel I Zhuravlev
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | | | - Naoto Hori
- Department of Chemistry, University of Texas at Austin, TX 78712, USA.
| | - Shaon Chakrabarti
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, TX 78712, USA. and Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
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15
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Reddy G, Thirumalai D. Collapse Precedes Folding in Denaturant-Dependent Assembly of Ubiquitin. J Phys Chem B 2017; 121:995-1009. [DOI: 10.1021/acs.jpcb.6b13100] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Govardhan Reddy
- Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - D. Thirumalai
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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16
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Maity H, Reddy G. Folding of Protein L with Implications for Collapse in the Denatured State Ensemble. J Am Chem Soc 2016; 138:2609-16. [PMID: 26835789 DOI: 10.1021/jacs.5b11300] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A fundamental question in protein folding is whether the coil to globule collapse transition occurs during the initial stages of folding (burst phase) or simultaneously with the protein folding transition. Single molecule fluorescence resonance energy transfer (FRET) and small-angle X-ray scattering (SAXS) experiments disagree on whether Protein L collapse transition occurs during the burst phase of folding. We study Protein L folding using a coarse-grained model and molecular dynamics simulations. The collapse transition in Protein L is found to be concomitant with the folding transition. In the burst phase of folding, we find that FRET experiments overestimate radius of gyration, Rg, of the protein due to the application of Gaussian polymer chain end-to-end distribution to extract Rg from the FRET efficiency. FRET experiments estimate ≈6 Å decrease in Rg when the actual decrease is ≈3 Å on guanidinium chloride denaturant dilution from 7.5 to 1 M, thereby suggesting pronounced compaction in the protein dimensions in the burst phase. The ≈3 Å decrease is close to the statistical uncertainties of the Rg data measured from SAXS experiments, which suggest no compaction, leading to a disagreement with the FRET experiments. The transition-state ensemble (TSE) structures in Protein L folding are globular and extensive in agreement with the Ψ-analysis experiments. The results support the hypothesis that the TSE of single domain proteins depends on protein topology and is not stabilized by local interactions alone.
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Affiliation(s)
- Hiranmay Maity
- Solid State and Structural Chemistry Unit, Indian Institute of Science , Bangalore, Karnataka 560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science , Bangalore, Karnataka 560012, India
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17
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Dave K, Jäger M, Nguyen H, Kelly JW, Gruebele M. High-Resolution Mapping of the Folding Transition State of a WW Domain. J Mol Biol 2016; 428:1617-36. [PMID: 26880334 DOI: 10.1016/j.jmb.2016.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 02/01/2016] [Accepted: 02/07/2016] [Indexed: 12/15/2022]
Abstract
Fast-folding WW domains are among the best-characterized systems for comparing experiments and simulations of protein folding. Recent microsecond-resolution experiments and long duration (totaling milliseconds) single-trajectory modeling have shown that even mechanistic changes in folding kinetics due to mutation can now be analyzed. Thus, a comprehensive set of experimental data would be helpful to benchmark the predictions made by simulations. Here, we use T-jump relaxation in conjunction with protein engineering and report mutational Φ-values (Φ(M)) as indicators for folding transition-state structure of 65 side chain, 7 backbone hydrogen bond, and 6 deletion and /or insertion mutants within loop 1 of the 34-residue hPin1 WW domain. Forty-five cross-validated consensus mutants could be identified that provide structural constraints for transition-state structure within all substructures of the WW domain fold (hydrophobic core, loop 1, loop 2, β-sheet). We probe the robustness of the two hydrophobic clusters in the folding transition state, discuss how local backbone disorder in the native-state can lead to non-classical Φ(M)-values (Φ(M) > 1) in the rate-determining loop 1 substructure, and conclusively identify mutations and positions along the sequence that perturb the folding mechanism from loop 1-limited toward loop 2-limited folding.
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Affiliation(s)
- Kapil Dave
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Marcus Jäger
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road BCC255, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road BCC255, La Jolla, CA 92037, USA
| | - Houbi Nguyen
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road BCC255, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road BCC255, La Jolla, CA 92037, USA
| | - Martin Gruebele
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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18
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Pal S, Bandyopadhyay S. Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms. J Chem Phys 2013; 139:235101. [DOI: 10.1063/1.4844255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Carter JW, Baker CM, Best RB, De Sancho D. Engineering folding dynamics from two-state to downhill: application to λ-repressor. J Phys Chem B 2013; 117:13435-43. [PMID: 24079652 PMCID: PMC3840902 DOI: 10.1021/jp405904g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
One
strategy for reaching the downhill folding regime, primarily
exploited for the λ6–85 protein fragment,
consists of cumulatively introducing mutations that speed up folding.
This is an experimentally demanding process where chemical intuition
usually serves as a guide for the choice of amino acid residues to
mutate. Such an approach can be aided by computational methods that
screen for protein engineering hot spots. Here we present one such
method that involves sampling the energy landscape of the pseudo-wild-type
protein and investigating the effect of point mutations on this landscape.
Using a novel metric for the cooperativity, we identify those residues
leading to the least cooperative folding. The folding dynamics of
the selected mutants are then directly characterized and the differences
in the kinetics are analyzed within a Markov-state model framework.
Although the method is general, here we present results for a coarse-grained
topology-based simulation model of λ-repressor, whose barrier
is reduced from an initial value of ∼4kBT at the midpoint to ∼1kBT, thereby reaching the downhill folding
regime.
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Affiliation(s)
- James W Carter
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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20
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Maffi C, Baiesi M, Casetti L, Piazza F, De Los Rios P. First-order coil-globule transition driven by vibrational entropy. Nat Commun 2013; 3:1065. [PMID: 22990861 DOI: 10.1038/ncomms2055] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 07/30/2012] [Indexed: 11/09/2022] Open
Abstract
By shifting the balance between conformational entropy and internal energy, polymers modify their shape under external stimuli, such as changes in temperature. Prominent among such transformations is the coil-globule transition, whereby a polymer can switch from an entropy-dominated coil conformation to a globular one, governed by energy. The nature of the coil-globule transition has remained elusive, with evidence for both continuous and discontinuous transitions, with the two-state behaviour of proteins as an instance of the latter. Theoretical models mostly predict second-order transitions. Here we introduce a model that takes into consideration hitherto neglected features common to any polymer. We show that a first-order phase transition smoothly appears as a function of the model parameters. Our results can relieve part of the conflicts between theory and experiments in the field of protein folding, in the wake of recent studies tracing back the remarkable properties of proteins to basic polymer physics.
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Affiliation(s)
- Carlo Maffi
- Laboratory of Statistical Biophysics, SB ITP, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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21
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Thirumalai D, Liu Z, O’Brien EP, Reddy G. Protein folding: from theory to practice. Curr Opin Struct Biol 2013; 23:22-9. [DOI: 10.1016/j.sbi.2012.11.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 11/27/2012] [Accepted: 11/28/2012] [Indexed: 01/26/2023]
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22
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Dasgupta A, Udgaonkar JB. Four-State Folding of a SH3 Domain: Salt-Induced Modulation of the Stabilities of the Intermediates and Native State. Biochemistry 2012; 51:4723-34. [DOI: 10.1021/bi300223b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amrita Dasgupta
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
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23
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Banerji A, Ghosh I. Fractal symmetry of protein interior: what have we learned? Cell Mol Life Sci 2011; 68:2711-37. [PMID: 21614471 PMCID: PMC11114926 DOI: 10.1007/s00018-011-0722-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 04/21/2011] [Accepted: 05/03/2011] [Indexed: 10/18/2022]
Abstract
The application of fractal dimension-based constructs to probe the protein interior dates back to the development of the concept of fractal dimension itself. Numerous approaches have been tried and tested over a course of (almost) 30 years with the aim of elucidating the various facets of symmetry of self-similarity prevalent in the protein interior. In the last 5 years especially, there has been a startling upsurge of research that innovatively stretches the limits of fractal-based studies to present an array of unexpected results on the biophysical properties of protein interior. In this article, we introduce readers to the fundamentals of fractals, reviewing the commonality (and the lack of it) between these approaches before exploring the patterns in the results that they produced. Clustering the approaches in major schools of protein self-similarity studies, we describe the evolution of fractal dimension-based methodologies. The genealogy of approaches (and results) presented here portrays a clear picture of the contemporary state of fractal-based studies in the context of the protein interior. To underline the utility of fractal dimension-based measures further, we have performed a correlation dimension analysis on all of the available non-redundant protein structures, both at the level of an individual protein and at the level of structural domains. In this investigation, we were able to separately quantify the self-similar symmetries in spatial correlation patterns amongst peptide-dipole units, charged amino acids, residues with the π-electron cloud and hydrophobic amino acids. The results revealed that electrostatic environments in the interiors of proteins belonging to 'α/α toroid' (all-α class) and 'PLP-dependent transferase-like' domains (α/β class) are highly conducive. In contrast, the interiors of 'zinc finger design' ('designed proteins') and 'knottins' ('small proteins') were identified as folds with the least conducive electrostatic environments. The fold 'conotoxins' (peptides) could be unambiguously identified as one type with the least stability. The same analyses revealed that peptide-dipoles in the α/β class of proteins, in general, are more correlated to each other than are the peptide-dipoles in proteins belonging to the all-α class. Highly favorable electrostatic milieu in the interiors of TIM-barrel, α/β-hydrolase structures could explain their remarkably conserved (evolutionary) stability from a new light. Finally, we point out certain inherent limitations of fractal constructs before attempting to identify the areas and problems where the implementation of fractal dimension-based constructs can be of paramount help to unearth latent information on protein structural properties.
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Affiliation(s)
- Anirban Banerji
- Bioinformatics Centre, University of Pune, Maharashtra, India.
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24
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Li MS, Co NT, Reddy G, Hu CK, Straub JE, Thirumalai D. Factors governing fibrillogenesis of polypeptide chains revealed by lattice models. PHYSICAL REVIEW LETTERS 2010; 105:218101. [PMID: 21231356 PMCID: PMC11298782 DOI: 10.1103/physrevlett.105.218101] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Indexed: 05/30/2023]
Abstract
Using lattice models we explore the factors that determine the tendencies of polypeptide chains to aggregate by exhaustively sampling the sequence and conformational space. The morphologies of the fibril-like structures and the time scales (τ(fib)) for their formation depend on a balance between hydrophobic and Coulomb interactions. The extent of population of an ensemble of N* structures, which are fibril-prone structures in the spectrum of conformations of an isolated protein, is the major determinant of τ(fib). This observation is used to determine the aggregating sequences by exhaustively exploring the sequence space, thus providing a basis for genome wide search of fragments that are aggregation prone.
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Affiliation(s)
- Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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25
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Desai TM, Cerminara M, Sadqi M, Muñoz V. The effect of electrostatics on the marginal cooperativity of an ultrafast folding protein. J Biol Chem 2010; 285:34549-56. [PMID: 20729560 DOI: 10.1074/jbc.m110.154021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins fold up by coordinating the different segments of their polypeptide chain through a network of weak cooperative interactions. Such cooperativity results in unfolding curves that are typically sigmoidal. However, we still do not know what factors modulate folding cooperativity or the minimal amount that ensures folding into specific three-dimensional structures. Here, we address these issues on BBL, a small helical protein that folds in microseconds via a marginally cooperative downhill process (Li, P., Oliva, F. Y., Naganathan, A. N., and Muñoz, V. (2009) Proc. Natl. Acad. Sci. USA. 106, 103-108). Particularly, we explore the effects of salt-induced screening of the electrostatic interactions in BBL at neutral pH and in acid-denatured BBL. Our results show that electrostatic screening stabilizes the native state of the neutral and protonated forms, inducing complete refolding of acid-denatured BBL. Furthermore, without net electrostatic interactions, the unfolding process becomes much less cooperative, as judged by the broadness of the equilibrium unfolding curve and the relaxation rate. Our experiments show that the marginally cooperative unfolding of BBL can still be made twice as broad while the protein retains its ability to fold into the native three-dimensional structure in microseconds. This result demonstrates experimentally that efficient folding does not require cooperativity, confirming predictions from theory and computer simulations and challenging the conventional biochemical paradigm. Furthermore, we conclude that electrostatic interactions are an important factor in determining folding cooperativity. Thus, electrostatic modulation by pH-salt and/or mutagenesis of charged residues emerges as an attractive tool for tuning folding cooperativity.
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Affiliation(s)
- Tanay M Desai
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, Madrid 28040, Spain
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26
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Abstract
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances in theory and experiments have resulted in a conceptual framework for describing the folding mechanisms of globular proteins. The sizes of proteins in the denatured and folded states, cooperativity of the folding transition, dispersions in the melting temperatures at the residue level, and timescales of folding are, to a large extent, determined by N, the number of residues. The intricate details of folding as a function of denaturant concentration can be predicted by using a novel coarse-grained molecular transfer model. By watching one molecule fold at a time, using single-molecule methods, investigators have established the validity of the theoretically anticipated heterogeneity in the folding routes and the N-dependent timescales for the three stages in the approach to the native state. Despite the successes of theory, of which only a few examples are documented here, we conclude that much remains to be done to solve the protein folding problem in the broadest sense.
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Affiliation(s)
- D Thirumalai
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
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27
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Sinha SK, Chakraborty S, Bandyopadhyay S. Secondary structure specific entropy change of a partially unfolded protein molecule. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:9911-9916. [PMID: 20405863 DOI: 10.1021/la1012389] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The conformational disorder of a protein in its partially unfolded molten globule (MG) form leads to an overall gain in the configurational entropy of the protein molecule. However, considering the differential degree of unfolding of different secondary structural segments of the protein, the entropy gained by them may be nonuniform. In this work, our attempt has been to explore whether any correlation exists between the degree of unfolding of different segments of a protein and their entropy gains. For that, we have carried out atomistic molecular dynamics simulations of the folded native and a partially unfolded structures of the protein villin headpiece subdomain or HP-36 in aqueous medium. It is found that among the three alpha-helical segments of the protein, the central alpha-helix (helix-2) underwent unfolding during the transition with a consequent entropy gain significantly higher than that of the other two helical segments. The calculations further revealed that the differential entropy gain by the segments of a protein can be used as an effective measure to identify the unfolded segments of the protein and hence to explore the folding pathways.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur -721302, India
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28
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Thanassoulas A, Nomikos M, Theodoridou M, Yannoukakos D, Mastellos D, Nounesis G. Thermodynamic study of the BRCT domain of BARD1 and its interaction with the -pSER-X-X-Phe- motif-containing BRIP1 peptide. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1908-16. [PMID: 20451671 DOI: 10.1016/j.bbapap.2010.04.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 04/15/2010] [Accepted: 04/26/2010] [Indexed: 01/14/2023]
Abstract
The BRCA1-associated RING domain protein 1 (BARD1) is the heterodimeric partner of BRCA1. The BRCA1/BARD1 complex demonstrates ubiquitin ligase activity and has been implicated in genomic stability and tumor suppression. Both proteins possess a structurally conserved C-terminal domain (BRCT). While BRCA1-BRCT has been shown to mediate BRCA1 interactions with phosphoproteins such as BRIP1 by recognizing the pSer-X-X-Phe motif, attempts to demonstrate analogous interactions of its dimeric counterpart BARD1-BRCT, have so far been unsuccessful. In this study, chemical-denaturation experiments of BARD1-BRCT domain suggest that its low thermodynamic stability (DeltaG=2.5 kcal/mol) at room temperature, may affect some of its biochemical properties, such as its interaction with phosphopeptides. The stability of BARD1-BRCT domain at 10 degrees C, increases to 7.5 kcal/mol and isothermal titration calorimetry (ITC) experiments at this lower temperature showed binding to the BRIP1 phosphopeptide via an enthalpy-driven interaction, which appears to be specific to the pSer-X-X-Phe peptide-binding motif. Substitution of either pSer at position 0 with Ser (non-phosphorylated peptide) or Phe with Val at position +3, leads to no-binding ITC results. While these findings are indicative that BRIP1 is a potential BARD1 binding partner, it becomes evident that in vitro binding assays involving the entire BARD1 protein and in vivo experiments are also needed to establish its binding partners and its potential role in tumor suppression pathways.
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Affiliation(s)
- Angelos Thanassoulas
- Biomolecular Physics Laboratory, IRRP, National Centre for Scientific Research "Demokritos", 153 10 Aghia Paraskevi, Greece
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29
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Makarov DE. Spatiotemporal correlations in denatured proteins: The dependence of fluorescence resonance energy transfer (FRET)-derived protein reconfiguration times on the location of the FRET probes. J Chem Phys 2010; 132:035104. [DOI: 10.1063/1.3284509] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Coexistence of flexibility and stability of proteins: an equation of state. PLoS One 2009; 4:e7296. [PMID: 19816577 PMCID: PMC2754529 DOI: 10.1371/journal.pone.0007296] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 08/24/2009] [Indexed: 11/19/2022] Open
Abstract
We consider a recently suggested “equation of state” for natively folded proteins, and verify its validity for a set of about 5800 proteins. The equation is based on a fractal viewpoint of proteins, on a generalization of the Landau-Peierls instability, and on a marginal stability criterion. The latter allows for coexistence of stability and flexibility of proteins, which is required for their proper function. The equation of state relates the protein fractal dimension , its spectral dimension , and the number of amino acids N. Using structural data from the protein data bank (PDB) and the Gaussian network model (GNM), we compute and for the entire set and demonstrate that the equation of state is well obeyed. Addressing the fractal properties and making use of the equation of state may help to engineer biologically inspired catalysts.
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31
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O'Brien EP, Brooks BR, Thirumalai D. Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins. Biochemistry 2009; 48:3743-54. [PMID: 19278261 DOI: 10.1021/bi8021119] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experiments show that for many two-state folders the free energy of the native state, DeltaG(ND)([C]), changes linearly as the denaturant concentration, [C], is varied. The slope {m = [dDeltaG(ND)([C])]/(d[C])}, is nearly constant. According to the transfer model, the m-value is associated with the difference in the surface area between the native (N) and denatured (D) state, which should be a function of DeltaR(g)(2), the difference in the square of the radius of gyration between the D and N states. Single-molecule experiments show that the R(g) of the structurally heterogeneous denatured state undergoes an equilibrium collapse transition as [C] decreases, which implies m also should be [C]-dependent. We resolve the conundrum between constant m-values and [C]-dependent changes in R(g) using molecular simulations of a coarse-grained representation of protein L, and the molecular transfer model, for which the equilibrium folding can be accurately calculated as a function of denaturant (urea) concentration. In agreement with experiment, we find that over a large range of denaturant concentration (>3 M) the m-value is a constant, whereas under strongly renaturing conditions (<3 M), it depends on [C]. The m-value is a constant above [C] > 3 M because the [C]-dependent changes in the surface area of the backbone groups, which make the largest contribution to m, are relatively narrow in the denatured state. The burial of the backbone and hydrophobic side chains gives rise to substantial surface area changes below [C] < 3 M, leading to collapse in the denatured state of protein L. Dissection of the contribution of various amino acids to the total surface area change with [C] shows that both the sequence context and residual structure are important. There are [C]-dependent variations in the surface area for chemically identical groups such as the backbone or Ala. Consequently, the midpoints of transition of individual residues vary significantly (which we call the Holtzer effect) even though global folding can be described as an all-or-none transition. The collapse is specific in nature, resulting in the formation of compact structures with appreciable populations of nativelike secondary structural elements. The collapse transition is driven by the loss of favorable residue-solvent interactions and a concomitant increase in the strength of intrapeptide interactions with a decreasing [C]. The strength of these interactions is nonuniformly distributed throughout the structure of protein L. Certain secondary structure elements have stronger [C]-dependent interactions than others in the denatured state.
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Affiliation(s)
- Edward P O'Brien
- Biophysics Program, Institute for Physical Science and Technology, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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32
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Fang HJ, Chen YZ, Li MS, Wu MC, Chang CL, Chang CK, Hsu YL, Huang TH, Chen HM, Tsong TY, Hu CK. Thermostability of the N-terminal RNA-binding domain of the SARS-CoV nucleocapsid protein: experiments and numerical simulations. Biophys J 2009; 96:1892-901. [PMID: 19254548 PMCID: PMC2717332 DOI: 10.1016/j.bpj.2008.10.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 10/15/2008] [Indexed: 10/25/2022] Open
Abstract
Differential scanning calorimetry, circular dichroism spectroscopy, nuclear magnetic resonance spectroscopy, and numerical simulations were used to study the thermostability of the N-terminal RNA-binding domain (RBD) of the SARS-CoV nucleocapsid protein. The transition temperature of the RBD in a mixing buffer, composed of glycine, sodium acetate, and sodium phosphate with 100 mM sodium chloride, at pH 6.8, determined by differential scanning calorimetry and circular dichroism, is 48.74 degrees C. Experimental results showed that the thermal-induced unfolding-folding transition of the RBD follows a two-state model with a reversibility >90%. Using a simple Gō-like model and Langevin dynamics we have shown that, in agreement with our experiments, the folding of the RBD is two-state. Theoretical estimates of thermodynamic quantities are in reasonable agreement with the experiments. Folding and thermal unfolding pathways of the RBD also were experimentally and numerically studied in detail. It was shown that the strand beta(1) from the N-terminal folds last and unfolds first, while the remaining beta-strands fold/unfold cooperatively.
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Affiliation(s)
- Huey-Jen Fang
- Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan
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33
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Abstract
The coil-globule transition, a tenet of the physics of polymers, has been identified in recent years as an important unresolved aspect of the initial stages of the folding of proteins. We describe the basics of the collapse transition, starting with homopolymers and continuing with proteins. Studies of denatured-state collapse under equilibrium are then presented. An emphasis is placed on single-molecule fluorescence experiments, which are particularly useful for measuring properties of the denatured state even under conditions of coexistence with the folded state. Attempts to understand the dynamics of collapse, both theoretically and experimentally, are then described. Only an upper limit for the rate of collapse has been obtained so far. Improvements in experimental and theoretical methodology are likely to continue to push our understanding of the importance of the denatured-state thermodynamics and dynamics for protein folding in the coming years.
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Affiliation(s)
- Guy Ziv
- Chemical Physics Department, Weizmann Institute of Science, 76100 Rehovot, Israel. E-mail:
| | - D. Thirumalai
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Gilad Haran
- Chemical Physics Department, Weizmann Institute of Science, 76100 Rehovot, Israel. E-mail:
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34
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Chen J, Bryngelson JD, Thirumalai D. Estimations of the Size of Nucleation Regions in Globular Proteins. J Phys Chem B 2008; 112:16115-20. [DOI: 10.1021/jp806161k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jie Chen
- Biophysics Program, Institute for Physical Science and Technology, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Physical Sciences Laboratory, Division of Computer Research and Technology, National Institutes of Health, Bethesda, Maryland 20892
| | - J. D. Bryngelson
- Biophysics Program, Institute for Physical Science and Technology, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Physical Sciences Laboratory, Division of Computer Research and Technology, National Institutes of Health, Bethesda, Maryland 20892
| | - D. Thirumalai
- Biophysics Program, Institute for Physical Science and Technology, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Physical Sciences Laboratory, Division of Computer Research and Technology, National Institutes of Health, Bethesda, Maryland 20892
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35
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Pawar A, Favrin G. Finite size effects in simulations of protein aggregation. PLoS One 2008; 3:e2641. [PMID: 18612385 PMCID: PMC2441439 DOI: 10.1371/journal.pone.0002641] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 05/26/2008] [Indexed: 11/30/2022] Open
Abstract
It is becoming increasingly clear that the soluble protofibrillar species that proceed amyloid fibril formation are associated with a range of neurodegenerative disorders such as Alzheimer's and Parkinson diseases. Computer simulations of the processes that lead to the formation of these oligomeric species are starting to make significant contributions to our understanding of the determinants of protein aggregation. We simulate different systems at constant concentration but with a different number of peptides and we study the how the finite number of proteins affects the underlying free energy of the system and therefore the relative stability of the species involved in the process. If not taken into account, this finite size effect can undermine the validity of theoretical predictions regarding the relative stability of the species involved and the rates of conversion from one to the other. We discuss the reasons that give rise to this finite size effect form both a probabilistic and energy fluctuations point of view and also how this problem can be dealt by a finite size scaling analysis.
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Affiliation(s)
- Amol Pawar
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Giorgio Favrin
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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36
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Ting CL, Makarov DE. Two-dimensional fluorescence resonance energy transfer as a probe for protein folding: A theoretical study. J Chem Phys 2008; 128:115102. [DOI: 10.1063/1.2835611] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Kouza M, Hu CK, Li MS. New force replica exchange method and protein folding pathways probed by force-clamp technique. J Chem Phys 2008; 128:045103. [DOI: 10.1063/1.2822272] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Bandyopadhyay S, Chakraborty S, Bagchi B. Coupling between hydration layer dynamics and unfolding kinetics of HP-36. J Chem Phys 2007; 125:084912. [PMID: 16965062 DOI: 10.1063/1.2335451] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We have performed atomistic molecular dynamics simulations of aqueous solutions of HP-36 at 300 K in its native state, as well as at high temperatures to explore the unfolding dynamics of the protein and its correlation with the motion of water around it. On increasing the temperature a partially unfolded molten globule state is formed where the smallest alpha helix (helix 2) unfolds into a coil. It is observed that the unfolding is initiated around the residue Phe-18 which shows a sharp displacement during unfolding. We have noticed that the unfolding of the protein affects the density of water near the protein surface. Besides, the dynamics of water in the protein hydration layer has been found to be strongly correlated with the time evolution of the unfolding process. We have introduced and calculated a displacement time correlation function to monitor the change in water motion relative to the protein backbone during unfolding. We find that the unfolding of helix 2 is associated with an increase in mobility of water around it as compared to water around the other two helices. We have also explored the microscopic aspects of secondary structure specific and site specific solvation dynamics of the protein. The calculations reveal that unfolding influences the solvation dynamics of the protein molecule in a heterogeneous manner depending on the location of the polar probe residues. This seems to be in agreement with recent experimental findings.
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Affiliation(s)
- Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India.
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39
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Li MS, Kouza M, Hu CK. Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin. Biophys J 2006; 92:547-61. [PMID: 17071662 PMCID: PMC1751401 DOI: 10.1529/biophysj.106.087684] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the C(alpha)-Gō model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. The force-quench refolding-times scale as tau(F) approximately exp(f(q)Deltax(F)/k(B)T), where f(q) is the quench force and Deltax(F) approximately 0.96 nm is the location of the average transition state along the reaction coordinate given by the end-to-end distance. This value is close to Deltax(F) approximately 0.8 nm obtained from the force-clamp experiments. The mechanical and thermal unfolding pathways are studied and compared with the experimental and all-atom simulation results in detail. The sequencing of thermal unfolding was found to be markedly different from the mechanical one. It is found that fixing the N-terminus of ubiquitin changes its mechanical unfolding pathways much more drastically compared to the case when the C-end is anchored. We obtained the distance between the native state and the transition state Deltax(UF) approximately 0.24 nm, which is in reasonable agreement with the experimental data.
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Affiliation(s)
- Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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40
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Nguyen PH, Stock G, Mittag E, Hu CK, Li MS. Free energy landscape and folding mechanism of a beta-hairpin in explicit water: a replica exchange molecular dynamics study. Proteins 2006; 61:795-808. [PMID: 16240446 DOI: 10.1002/prot.20696] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The free energy landscape and the folding mechanism of the C-terminal beta-hairpin of protein G is studied by extensive replica exchange molecular dynamics simulations (40 replicas and 340 ns total simulation time), using the GROMOS96 force field and the SPC explicit water solvent. The study reveals that the system preferentially adopts a beta-hairpin structure at biologically important temperatures, and that the helix content is low at all temperatures studied. Representing the free energy landscape as a function of several types of reaction coordinates, four local minima corresponding to the folded, partially folded, molten globule, and unfolded states are identified. The findings suggest that the folding of the beta-hairpin occurs as the sequence: collapse of hydrophobic core --> formation of H-bond --> formation of the turn. Identifying the folded and molten globule states as the main conformations, the free energy landscape of the beta-hairpin is consistent with a two-state behavior with a broad transition state. The temperature dependence of the folding-unfolding transition is investigated in some detail. The enthalpy and entropy jumps at the folding transition temperature are found to be about three times lower than the experimental estimates, indicating that the folding-unfolding transition in silico is less cooperative than its in vitro counterpart.
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Affiliation(s)
- Phuong H Nguyen
- Institute of Physical and Theoretical Chemistry, J.W. Goethe University, Frankfurt, Germany.
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41
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Liu Z, Chan HS. Solvation and desolvation effects in protein folding: native flexibility, kinetic cooperativity and enthalpic barriers under isostability conditions. Phys Biol 2005; 2:S75-85. [PMID: 16280624 DOI: 10.1088/1478-3975/2/4/s01] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
As different parts of a protein chain approach one another during folding, they are expected to encounter desolvation barriers before optimal packing is achieved. This impediment originates from the water molecule's finite size, which entails a net energetic cost for water exclusion when the formation of compensating close intraprotein contacts is not yet complete. Based on recent advances, we extend our exploration of these microscopic elementary desolvation barriers' roles in the emergence of generic properties of protein folding. Using continuum Gō-like C(alpha) chain models of chymotrypsin inhibitor 2 (CI2) and barnase as examples, we underscore that elementary desolvation barriers between a protein's constituent groups can significantly reduce native conformational fluctuations relative to model predictions that neglected these barriers. An increasing height of elementary desolvation barriers leads to thermodynamically more cooperative folding/unfolding transitions (i.e., higher overall empirical folding barriers) and higher degrees of kinetic cooperativity as manifested by more linear rate-stability relationships under constant temperature. Applying a spatially non-uniform thermodynamic parametrization we recently introduced for the pairwise C(alpha) potentials of mean force, the present barnase model further illustrates that desolvation is a probable physical underpinning for the experimentally observed high intrinsic enthalpic folding barrier under isostability conditions.
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Affiliation(s)
- Zhirong Liu
- Department of Biochemistry, and Department of Medical Genetics & Microbiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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42
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Abstract
The folding of the alpha-helix domain hbSBD of the mammalian mitochondrial branched-chain alpha-ketoacid dehydrogenase complex is studied by the circular dichroism technique in absence of urea. Thermal denaturation is used to evaluate various thermodynamic parameters defining the equilibrium unfolding, which is well described by the two-state model with the folding temperature T(F) = 317.8 +/- 1.95 K and the enthalpy change DeltaH(G) = 19.67 +/- 2.67 kcal/mol. The folding is also studied numerically using the off-lattice coarse-grained Go model and the Langevin dynamics. The obtained results, including the population of the native basin, the free-energy landscape as a function of the number of native contacts, and the folding kinetics, also suggest that the hbSBD domain is a two-state folder. These results are consistent with the biological function of hbSBD in branched-chain alpha-ketoacid dehydrogenase.
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Affiliation(s)
- Maksim Kouza
- Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw, Poland
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