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Yanaka S, Yagi-Utsumi M, Kato K, Kuwajima K. The B domain of protein A retains residual structures in 6 M guanidinium chloride as revealed by hydrogen/deuterium-exchange NMR spectroscopy. Protein Sci 2023; 32:e4569. [PMID: 36659853 PMCID: PMC9926473 DOI: 10.1002/pro.4569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
The characterization of residual structures persistent in unfolded proteins is an important issue in studies of protein folding, because the residual structures present, if any, may form a folding initiation site and guide the subsequent folding reactions. Here, we studied the residual structures of the isolated B domain (BDPA) of staphylococcal protein A in 6 M guanidinium chloride. BDPA is a small three-helix-bundle protein, and until recently its folding/unfolding reaction has been treated as a simple two-state process between the native and the fully unfolded states. We employed a dimethylsulfoxide (DMSO)-quenched hydrogen/deuterium (H/D)-exchange 2D NMR techniques with the use of spin desalting columns, which allowed us to investigate the H/D-exchange behavior of individually identified peptide amide (NH) protons. We obtained H/D-exchange protection factors of the 21 NH protons that form an α-helical hydrogen bond in the native structure, and the majority of these NH protons were significantly protected with a protection factor of 2.0-5.2 in 6 M guanidinium chloride, strongly suggesting that these weakly protected NH protons form much stronger hydrogen bonds under native folding conditions. The results can be used to deduce the structure of an early folding intermediate, when such an intermediate is shown by other methods. Among three native helical regions, the third helix in the C-terminal side was highly protected and stabilized by side-chain salt bridges, probably acting as the folding initiation site of BDPA. The present results are discussed in relation to previous experimental and computational findings on the folding mechanisms of BDPA.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Kunihiro Kuwajima
- Department of Physics, School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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2
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Xue M, Wakamoto T, Kejlberg C, Yoshimura Y, Nielsen TA, Risør MW, Sanggaard KW, Kitahara R, Mulder FAA. How internal cavities destabilize a protein. Proc Natl Acad Sci U S A 2019; 116:21031-6. [PMID: 31570587 DOI: 10.1073/pnas.1911181116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although many proteins possess a distinct folded structure lying at a minimum in a funneled free energy landscape, thermal energy causes any protein to continuously access lowly populated excited states. The existence of excited states is an integral part of biological function. Although transitions into the excited states may lead to protein misfolding and aggregation, little structural information is currently available for them. Here, we show how NMR spectroscopy, coupled with pressure perturbation, brings these elusive species to light. As pressure acts to favor states with lower partial molar volume, NMR follows the ensuing change in the equilibrium spectroscopically, with residue-specific resolution. For T4 lysozyme L99A, relaxation dispersion NMR was used to follow the increase in population of a previously identified "invisible" folded state with pressure, as this is driven by the reduction in cavity volume by the flipping-in of a surface aromatic group. Furthermore, multiple partly disordered excited states were detected at equilibrium using pressure-dependent H/D exchange NMR spectroscopy. Here, unfolding reduced partial molar volume by the removal of empty internal cavities and packing imperfections through subglobal and global unfolding. A close correspondence was found for the distinct pressure sensitivities of various parts of the protein and the amount of internal cavity volume that was lost in each unfolding event. The free energies and populations of excited states allowed us to determine the energetic penalty of empty internal protein cavities to be 36 cal⋅Å-3.
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3
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Peran I, Holehouse AS, Carrico IS, Pappu RV, Bilsel O, Raleigh DP. Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random coil-like dimensions. Proc Natl Acad Sci U S A 2019; 116:12301-10. [PMID: 31167941 DOI: 10.1073/pnas.1818206116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Proteins are marginally stable molecules that fluctuate between folded and unfolded states. Here, we provide a high-resolution description of unfolded states under refolding conditions for the N-terminal domain of the L9 protein (NTL9). We use a combination of time-resolved Förster resonance energy transfer (FRET) based on multiple pairs of minimally perturbing labels, time-resolved small-angle X-ray scattering (SAXS), all-atom simulations, and polymer theory. Upon dilution from high denaturant, the unfolded state undergoes rapid contraction. Although this contraction occurs before the folding transition, the unfolded state remains considerably more expanded than the folded state and accommodates a range of local and nonlocal contacts, including secondary structures and native and nonnative interactions. Paradoxically, despite discernible sequence-specific conformational preferences, the ensemble-averaged properties of unfolded states are consistent with those of canonical random coils, namely polymers in indifferent (theta) solvents. These findings are concordant with theoretical predictions based on coarse-grained models and inferences drawn from single-molecule experiments regarding the sequence-specific scaling behavior of unfolded proteins under folding conditions.
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4
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Riback JA, Bowman MA, Zmyslowski AM, Plaxco KW, Clark PL, Sosnick TR. Commonly used FRET fluorophores promote collapse of an otherwise disordered protein. Proc Natl Acad Sci U S A 2019; 116:8889-94. [PMID: 30992378 DOI: 10.1073/pnas.1813038116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The dimensions that unfolded proteins, including intrinsically disordered proteins (IDPs), adopt in the absence of denaturant remain controversial. We developed an analysis procedure for small-angle X-ray scattering (SAXS) profiles and used it to demonstrate that even relatively hydrophobic IDPs remain nearly as expanded in water as they are in high denaturant concentrations. In contrast, as demonstrated here, most fluorescence resonance energy transfer (FRET) measurements have indicated that relatively hydrophobic IDPs contract significantly in the absence of denaturant. We use two independent approaches to further explore this controversy. First, using SAXS we show that fluorophores employed in FRET can contribute to the observed discrepancy. Specifically, we find that addition of Alexa-488 to a normally expanded IDP causes contraction by an additional 15%, a value in reasonable accord with the contraction reported in FRET-based studies. Second, using our simulations and analysis procedure to accurately extract both the radius of gyration (Rg) and end-to-end distance (Ree) from SAXS profiles, we tested the recent suggestion that FRET and SAXS results can be reconciled if the Rg and Ree are "uncoupled" (i.e., no longer simply proportional), in contrast to the case for random walk homopolymers. We find, however, that even for unfolded proteins, these two measures of unfolded state dimensions remain proportional. Together, these results suggest that improved analysis procedures and a correction for significant, fluorophore-driven interactions are sufficient to reconcile prior SAXS and FRET studies, thus providing a unified picture of the nature of unfolded polypeptide chains in the absence of denaturant.
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5
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Guinn EJ, Marqusee S. Exploring the Denatured State Ensemble by Single-Molecule Chemo-Mechanical Unfolding: The Effect of Force, Temperature, and Urea. J Mol Biol 2018; 430:450-64. [PMID: 28782558 DOI: 10.1016/j.jmb.2017.07.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/29/2017] [Accepted: 07/31/2017] [Indexed: 11/22/2022]
Abstract
While it is widely appreciated that the denatured state of a protein is a heterogeneous conformational ensemble, there is still debate over how this ensemble changes with environmental conditions. Here, we use single-molecule chemo-mechanical unfolding, which combines force and urea using the optical tweezers, together with traditional protein unfolding studies to explore how perturbants commonly used to unfold proteins (urea, force, and temperature) affect the denatured-state ensemble. We compare the urea m-values, which report on the change in solvent accessible surface area for unfolding, to probe the denatured state as a function of force, temperature, and urea. We find that while the urea- and force-induced denatured states expose similar amounts of surface area, the denatured state at high temperature and low urea concentration is more compact. To disentangle these two effects, we use destabilizing mutations that shift the Tm and Cm. We find that the compaction of the denatured state is related to changing temperature as the different variants of acyl-coenzyme A binding protein have similar m-values when they are at the same temperature but different urea concentration. These results have important implications for protein folding and stability under different environmental conditions.
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6
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Zou J, Song B, Simmerling C, Raleigh D. Experimental and Computational Analysis of Protein Stabilization by Gly-to-d-Ala Substitution: A Convolution of Native State and Unfolded State Effects. J Am Chem Soc 2016; 138:15682-15689. [PMID: 27934019 PMCID: PMC5442443 DOI: 10.1021/jacs.6b09511] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The rational and predictable enhancement of protein stability is an important goal in protein design. Most efforts target the folded state, however stability is the free energy difference between the folded and unfolded states thus both are suitable targets. Strategies directed at the unfolded state usually seek to decrease chain entropy by introducing cross-links or by replacing glycines. Cross-linking has led to mixed results. Replacement of glycine with an l-amino acid, while reducing the entropy of the unfolded state, can introduce unfavorable steric interactions in the folded state, since glycine is often found in conformations that require a positive φ angle such as helical C-capping motifs or type I' and II″ β-turns. l-Amino acids are strongly disfavored in these conformations, but d-amino acids are not. However, there are few reported examples and conflicting results have been obtained when glycines are replaced with d-Ala. We critically examine the effect of Gly-to-d-Ala substitutions on protein stability using experimental approaches together with molecular dynamics simulations and free energy calculations. The data, together with a survey of high resolution structures, show that the vast majority of proteins can be stabilized by substitution of C-capping glycines with d-Ala. Sites suitable for substitutions can be identified via sequence alignment with a high degree of success. Steric clashes in the native state due to the new side chain are rarely observed, but are likely responsible for the destabilizing or null effect observed for the small subset of Gly-to-d-Ala substitutions which are not stabilizing. Changes in backbone solvation play less of a role. Favorable candidates for d-Ala substitution can be identified using a rapid algorithm based on molecular mechanics.
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Affiliation(s)
- Junjie Zou
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Benben Song
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400
| | - Daniel Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
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7
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Abstract
Glycosylation plays not only a functional role but can also modify the biophysical properties of the modified protein. Usually, natural glycosylation results in protein stabilization; however, in vitro and in silico studies showed that sometimes glycosylation results in thermodynamic destabilization. Here, we applied coarse-grained and all-atom molecular dynamics simulations to understand the mechanism underlying the loss of stability of the MM1 protein by glycosylation. We show that the origin of the destabilization is a conformational distortion of the protein caused by the interaction of the monosaccharide with the protein surface. Though glycosylation creates new short-range glycan-protein interactions that stabilize the conjugated protein, it breaks long-range protein-protein interactions. This has a destabilizing effect because the probability of long- and short-range interactions forming differs between the folded and unfolded states. The destabilization originates not from simple loss of interactions but due to a trade-off between the short- and long-range interactions.
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Affiliation(s)
- Yulian Gavrilov
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Dalit Shental-Bechor
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
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8
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Abstract
A fundamental open problem in biophysics is how the folded structure of the main chain (MC) of a protein is determined by the physics of the interactions between the side chains (SCs). All-atom molecular dynamics simulations of a model protein (Trp-cage) revealed that strong correlations between the motions of the SCs and the MC occur transiently at 380 K in unfolded segments of the protein and during the simulations of the whole amino-acid sequence at 450 K. The high correlation between the SC and MC fluctuations is a fundamental property of the unfolded state and is also relevant to unstructured proteins as intrinsically disordered proteins (IDPs), for which new reaction coordinates are introduced. The presented findings may open a new door as to how functions of IDPs are related to conformations, which play a crucial role in neurodegenerative diseases.
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9
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Skinner JJ, Yu W, Gichana EK, Baxa MC, Hinshaw JR, Freed KF, Sosnick TR. Benchmarking all-atom simulations using hydrogen exchange. Proc Natl Acad Sci U S A 2014; 111:15975-80. [PMID: 25349413 DOI: 10.1073/pnas.1404213111] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517-520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.
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10
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Foderà V, Vetri V, Wind TS, Noppe W, Cornett C, Donald AM, Morozova-Roche LA, Vestergaard B. Observation of the Early Structural Changes Leading to the Formation of Protein Superstructures. J Phys Chem Lett 2014; 5:3254-3258. [PMID: 26276341 DOI: 10.1021/jz501614e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Formation of superstructures in protein aggregation processes has been indicated as a general pathway for several proteins, possibly playing a role in human pathologies. There is a severe lack of knowledge on the origin of such species in terms of both mechanisms of formation and structural features. We use equine lysozyme as a model protein, and by combining spectroscopic techniques and microscopy with X-ray fiber diffraction and ab initio modeling of Small Angle X-ray Scattering data, we isolate the partially unfolded state from which one of these superstructures (i.e., particulate) originates. We reveal the low-resolution structure of the unfolded state and its mechanism of formation, highlighting the physicochemical features and the possible pathway of formation of the particulate structure. Our findings provide a novel detailed knowledge of such a general and alternative aggregation pathway for proteins, this being crucial for a basic and broader understanding of the aggregation phenomena.
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Affiliation(s)
- Vito Foderà
- ‡Sector of Biological and Soft Systems, Department of Physics, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Valeria Vetri
- §Dipartimento di Fisica e Chimica, Universitá di Palermo, Viale delle Scienze, Edificio 18, 90128 Palermo, Italy
| | | | - Wim Noppe
- ∥IRF Life Sciences, KuLeuven KULAK, Etienne Sabbelaan 53, 8500 Kortrijk, Belgium
| | | | - Athene M Donald
- ‡Sector of Biological and Soft Systems, Department of Physics, Cavendish Laboratory, University of Cambridge, 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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11
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Kathuria SV, Kayatekin C, Barrea R, Kondrashkina E, Graceffa R, Guo L, Nobrega RP, Chakravarthy S, Matthews CR, Irving TC, Bilsel O. Microsecond barrier-limited chain collapse observed by time-resolved FRET and SAXS. J Mol Biol 2014; 426:1980-94. [PMID: 24607691 DOI: 10.1016/j.jmb.2014.02.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 02/14/2014] [Accepted: 02/24/2014] [Indexed: 01/08/2023]
Abstract
It is generally held that random-coil polypeptide chains undergo a barrier-less continuous collapse when the solvent conditions are changed to favor the fully folded native conformation. We test this hypothesis by probing intramolecular distance distributions during folding in one of the paradigms of folding reactions, that of cytochrome c. The Trp59-to-heme distance was probed by time-resolved Förster resonance energy transfer in the microsecond time range of refolding. Contrary to expectation, a state with a Trp59-heme distance close to that of the guanidinium hydrochloride (GdnHCl) denatured state is present after ~27 μs of folding. A concomitant decrease in the population of this state and an increase in the population of a compact high-FRET (Förster resonance energy transfer) state (efficiency>90%) show that the collapse is barrier limited. Small-angle X-ray scattering (SAXS) measurements over a similar time range show that the radius of gyration under native favoring conditions is comparable to that of the GdnHCl denatured unfolded state. An independent comprehensive global thermodynamic analysis reveals that marginally stable partially folded structures are also present in the nominally unfolded GdnHCl denatured state. These observations suggest that specifically collapsed intermediate structures with low stability in rapid equilibrium with the unfolded state may contribute to the apparent chain contraction observed in previous fluorescence studies using steady-state detection. In the absence of significant dynamic averaging of marginally stable partially folded states and with the use of probes sensitive to distance distributions, barrier-limited chain contraction is observed upon transfer of the GdnHCl denatured state ensemble to native-like conditions.
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Affiliation(s)
- Sagar V Kathuria
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Can Kayatekin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Raul Barrea
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | | | - Rita Graceffa
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Liang Guo
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - R Paul Nobrega
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - C Robert Matthews
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Thomas C Irving
- BioCAT, CSRRI, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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12
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Abstract
The growing recognition of the many roles that disordered protein states play in biology places an increasing importance on developing approaches to characterize the structural properties of this class of proteins and to clarify the links between these properties and the associated biological functions. Disordered proteins, when isolated in solution, do not adopt a fixed structure, but can and often do contain detectable and significant residual or transient structure, including both secondary and long-range structure. Such residual structure can play a role in nucleating local structural transitions as well as modulating intramolecular or intermolecular tertiary interactions, including those involved in ordered protein aggregation. An increasing array of tools has been recruited to help characterize the structural properties of disordered proteins. While a number of methods can report on residual secondary structure, detecting and quantifying transient long-range structure has proven to be more difficult. This chapter describes the use of paramagnetic spin labeling in combination with paramagnetic relaxation enhancement (PRE) in NMR spectroscopy and pulsed dipolar ESR spectroscopy (PDS) for this purpose.
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Affiliation(s)
- David Eliezer
- Department of Biochemistry and Program in Structural Biology, Weill Cornell Medical College, New York, NY, USA.
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13
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Marsh JA, Forman-Kay JD. Ensemble modeling of protein disordered states: experimental restraint contributions and validation. Proteins 2011; 80:556-72. [PMID: 22095648 DOI: 10.1002/prot.23220] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 10/11/2011] [Indexed: 12/13/2022]
Abstract
Disordered states of proteins include the biologically functional intrinsically disordered proteins and the unfolded states of normally folded proteins. In recent years, ensemble-modeling strategies using various experimental measurements as restraints have emerged as powerful means for structurally characterizing disordered states. However, these methods are still in their infancy compared with the structural determination of folded proteins. Here, we have addressed several issues important to ensemble modeling using our ENSEMBLE methodology. First, we assessed how calculating ensembles containing different numbers of conformers affects their structural properties. We find that larger ensembles have very similar properties to smaller ensembles fit to the same experimental restraints, thus allowing a considerable speed improvement in our calculations. In addition, we analyzed the contributions of different experimental restraints to the structural properties of calculated ensembles, enabling us to make recommendations about the experimental measurements that should be made for optimal ensemble modeling. The effects of different restraints, most significantly from chemical shifts, paramagnetic relaxation enhancements and small-angle X-ray scattering, but also from other data, underscore the importance of utilizing multiple sources of experimental data. Finally, we validate our ENSEMBLE methodology using both cross-validation and synthetic experimental restraints calculated from simulated ensembles. Our results suggest that secondary structure and molecular size distribution can generally be modeled very accurately, whereas the accuracy of calculated tertiary structure is dependent on the number of distance restraints used.
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Affiliation(s)
- Joseph A Marsh
- Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; MRC Laboratory of Molecular Biology, Cambridge CB2 02H, United Kingdom
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14
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Cho JH, Sato S, Horng JC, Anil B, Raleigh DP. Electrostatic interactions in the denatured state ensemble: their effect upon protein folding and protein stability. Arch Biochem Biophys 2008; 469:20-8. [PMID: 17900519 PMCID: PMC2820407 DOI: 10.1016/j.abb.2007.08.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 07/19/2007] [Accepted: 08/01/2007] [Indexed: 11/17/2022]
Abstract
It is now recognized that the denatured state ensemble (DSE) of proteins can contain significant amounts of structure, particularly under native conditions. Well-studied examples include small units of hydrogen bonded secondary structure, particularly helices or turns as well as hydrophobic clusters. Other types of interactions are less well characterized and it has often been assumed that electrostatic interactions play at most a minor role in the DSE. However, recent studies have shown that both favorable and unfavorable electrostatic interactions can be formed in the DSE. These can include surprisingly specific non-native interactions that can even persist in the transition state for protein folding. DSE electrostatic interactions can be energetically significant and their modulation either by mutation or by varying solution conditions can have a major impact upon protein stability. pH dependent stability studies have shown that electrostatic interactions can contribute up to 4 kcal mol(-1) to the stability of the DSE.
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Affiliation(s)
- Jae-Hyun Cho
- Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA,
| | - Satoshi Sato
- Okayama Research Park Incubation Center, 5303 Haga Okayama 701-1221 JAPAN,
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Taiwan 30013 R.O.C,
| | - Burcu Anil
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook NY 11794-3400, USA,
| | - Daniel P. Raleigh
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook NY 11794-3400, USA,
- Graduate Program in Biophysics, Graduate Program in Biochemistry and Structural Biology, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
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15
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Abstract
The importance of disordered protein states in biology is gaining recognition, and can be attributed in part to the participation of unfolded and partially folded states of globular proteins in normal and abnormal biological functions, such as protein translation, protein translocation, protein degradation, protein assembly, and protein aggregation (1-5). There is also a growing awareness that a significant fraction of gene products from various genomes, including the human genome, fall into a category that includes low complexity, low globularity, or intrinsically unstructured proteins (6-9). Unlike native states of globular proteins, disordered protein states, by definition, do not adopt a fixed structure that can be determined using classical high-resolution methods. Nevertheless, there has long been evidence that many disordered states contain detectable and significant residual or nascent structure (10-16). This structure has been found to be important for nucleating local structure, as well as mediating long range contacts upon either intramolecular folding to the native state (17-21) or intermolecular folding with specific binding partners (22-24), and is also predicted to influence intermolecular folding into structured aggregates (25,26). The primary tool for the characterization of such structure is high-resolution solution state nuclear magnetic resonance (NMR) spectroscopy. Advances in NMR instrumentation and methods have greatly facilitated this task and in principle can now be accomplished by those without extensive prior experience in NMR spectroscopy. This chapter describes how this can be accomplished.
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Affiliation(s)
- David Eliezer
- Department of Biochemistry and Program in Structural Biology, Weill Medical College of Cornell University, New York, NY, USA
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16
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Geierhaas CD, Nickson AA, Lindorff-Larsen K, Clarke J, Vendruscolo M. BPPred: a Web-based computational tool for predicting biophysical parameters of proteins. Protein Sci 2007; 16:125-34. [PMID: 17123959 PMCID: PMC2222837 DOI: 10.1110/ps.062383807] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 09/17/2006] [Accepted: 09/18/2006] [Indexed: 10/23/2022]
Abstract
We exploit the availability of recent experimental data on a variety of proteins to develop a Web-based prediction algorithm (BPPred) to calculate several biophysical parameters commonly used to describe the folding process. These parameters include the equilibrium m-values, the length of proteins, and the changes upon unfolding in the solvent-accessible surface area, in the heat capacity, and in the radius of gyration. We also show that the knowledge of any one of these quantities allows an estimate of the others to be obtained, and describe the confidence limits with which these estimations can be made. Furthermore, we discuss how the kinetic m-values, or the Beta Tanford values, may provide an estimate of the solvent-accessible surface area and the radius of gyration of the transition state for protein folding. Taken together, these results suggest that BPPred should represent a valuable tool for interpreting experimental measurements, as well as the results of molecular dynamics simulations.
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Bhavesh NS, Juneja J, Udgaonkar JB, Hosur RV. Native and nonnative conformational preferences in the urea- unfolded state of barstar. Protein Sci 2004; 13:3085-91. [PMID: 15537753 PMCID: PMC2287308 DOI: 10.1110/ps.04805204] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Revised: 07/12/2004] [Accepted: 08/14/2004] [Indexed: 10/26/2022]
Abstract
The refolding of barstar from its urea-unfolded state has been studied extensively using various spectroscopic probes and real-time NMR, which provide global and residue-specific information, respectively, about the folding process. Here, a preliminary structural characterization by NMR of barstar in 8 M urea has been carried out at pH 6.5 and 25 degrees C. Complete backbone resonance assignments of the urea-unfolded protein were obtained using the recently developed three-dimensional NMR techniques of HNN and HN(C)N. The conformational propensities of the polypeptide backbone in the presence of 8 M urea have been estimated by examining deviations of secondary chemical shifts from random coil values. For some residues that belong to helices in native barstar, 13C(alpha) and 13CO secondary shifts show positive deviations in the urea-unfolded state, indicating that these residues have propensities toward helical conformations. These residues are, however, juxtaposed by residues that display negative deviations indicative of propensities toward extended conformations. Thus, segments that are helical in native barstar are unlikely to preferentially populate the helical conformation in the unfolded state. Similarly, residues belonging to beta-strands 1 and 2 of native barstar do not appear to show any conformational preferences in the unfolded state. On the other hand, residues belonging to the beta-strand 3 segment show weak nonnative helical conformational preferences in the unfolded state, indicating that this segment may possess a weak preference for populating a helical conformation in the unfolded state.
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Affiliation(s)
- Neel S Bhavesh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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Bhutani N, Udgaonkar JB. Folding subdomains of thioredoxin characterized by native-state hydrogen exchange. Protein Sci 2003; 12:1719-31. [PMID: 12876321 PMCID: PMC2323958 DOI: 10.1110/ps.0239503] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2002] [Revised: 05/02/2003] [Accepted: 05/02/2003] [Indexed: 10/26/2022]
Abstract
Native-state hydrogen exchange (HX) studies, used in conjunction with NMR spectroscopy, have been carried out on Escherichia coli thioredoxin (Trx) for characterizing two folding subdomains of the protein. The backbone amide protons of only the slowest-exchanging 24 amino acid residues, of a total of 108 amino acid residues, could be followed at pH 7. The free energy of the opening event that results in an amide hydrogen exchanging with solvent (DeltaG(op)) was determined at each of the 24 amide hydrogen sites. The values of DeltaG(op) for the amide hydrogens belonging to residues in the helices alpha(1), alpha(2), and alpha(4) are consistent with them exchanging with the solvent only when the fully unfolded state is sampled transiently under native conditions. The denaturant-dependences of the values of DeltaG(op) provide very little evidence that the protein samples partially unfolded forms, lower in energy than the unfolded state. The amide hydrogens belonging to the residues in the beta strands, which form the core of the protein, appear to have higher values of DeltaG(op) than amide hydrogens belonging to residues in the helices, suggesting that they might be more stable to exchange. This apparently higher stability to HX of the beta strands might be either because they exchange out their amide hydrogens in a high energy intermediate preceding the globally unfolded state, or, more likely, because they form residual structure in the globally unfolded state. In either case, the central beta strands-beta(3,) beta(2), and beta(4)-would appear to form a cooperatively folding subunit of the protein. The native-state HX methodology has made it possible to characterize the free energy landscape that Trx can sample under equilibrium native conditions.
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Affiliation(s)
- Nidhi Bhutani
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, University of Agricultural Sciences at the Gandhi Krishi Vigyan Kendra Campus, Bangalore 560065, India
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Cavalli A, Haberthür U, Paci E, Caflisch A. Fast protein folding on downhill energy landscape. Protein Sci 2003; 12:1801-3. [PMID: 12876329 PMCID: PMC2323966 DOI: 10.1110/ps.0366103] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2003] [Revised: 05/01/2003] [Accepted: 05/01/2003] [Indexed: 10/26/2022]
Abstract
Proteins fold in a time range of microseconds to minutes despite the large amount of possible conformers. Molecular dynamics simulations of a three-stranded antiparallel beta-sheet peptide (for a total of 12.6 microsec and 72 folding events) show that at the melting temperature the unfolded state ensemble contains many more conformers than those sampled during a folding event.
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Affiliation(s)
- Andrea Cavalli
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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