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Kuczera K, Szoszkiewicz R, Shaffer CL, Jas GS. GB1 hairpin kinetics: capturing the folding pathway with molecular dynamics, replica exchange and optimal dimensionality reduction. J Biomol Struct Dyn 2023; 41:11671-11680. [PMID: 36591705 DOI: 10.1080/07391102.2022.2163427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/22/2022] [Indexed: 01/03/2023]
Abstract
We have performed molecular dynamics (MD) and replica-exchange (REMD) simulations of folding of the GB1 hairpin peptide in aqueous solution. REMD results were consistent with a cooperative zipper folding model. 120 μ s MD trajectories at 320 K yielded relaxation times of 1.8 μ s and 100 ns, with the slower assigned to global folding. The MD folding/unfolding transitions also followed the cooperative zipper model, specifying nucleation at the central turn followed by consecutive hydrogen bond formation. Formation of hydrogen bonds and hydrophobic contacts were highly correlated. Coarse-grained kinetic models constructed with the Optimal Dimensionality Reduction (ODR) approach found a folding time of 3.3 μ s and unfolding time of 4.0 μ s . Additionally, relaxation times in the 130-170 ns range could be assigned to formation of the transition state and off-path intermediates. The unfolded state was the most highly populated and, significantly, most heterogenous, assembling the largest number of microstates, primarily composed of extended and turn structures. The folded state was also heterogenous, but a to a lesser degree, involving the fully folded and partially folded in-register hairpins at early stages of the zipper pathway. The transition state corresponded to the nucleated hairpin, with central turn and first beta-sheet hydrogen bond, while the off-path intermediates were off-register partial hairpins. Our simulation results were in excellent agreement with experimental data on folded fraction, relaxation time and folding mechanism. The new findings from this work suggest a highly cooperative zipper folding mechanism, nascent hairpin transition state and ∼100 ns relaxation related to intermediate formation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Krzysztof Kuczera
- Department of Chemistry, The University of Kansas, Lawrence, KS, USA
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Robert Szoszkiewicz
- Faculty of Chemistry, Biological and Chemical Research Centre University of Warsaw, Warsaw, Poland
| | - Christopher L Shaffer
- College of Pharmacy and Pediatric Clinical Pharmacology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Gouri S Jas
- College of Pharmacy and Pediatric Clinical Pharmacology, University of Nebraska Medical Center, Omaha, NE, USA
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Dale JB, Smeesters PR, Courtney HS, Penfound TA, Hohn CM, Smith JC, Baudry JY. Structure-based design of broadly protective group a streptococcal M protein-based vaccines. Vaccine 2016; 35:19-26. [PMID: 27890396 DOI: 10.1016/j.vaccine.2016.11.065] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/10/2016] [Accepted: 11/17/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND A major obstacle to the development of broadly protective M protein-based group A streptococcal (GAS) vaccines is the variability within the N-terminal epitopes that evoke potent bactericidal antibodies. The concept of M type-specific protective immune responses has recently been challenged based on the observation that multivalent M protein vaccines elicited cross-reactive bactericidal antibodies against a number of non-vaccine M types of GAS. Additionally, a new "cluster-based" typing system of 175M proteins identified a limited number of clusters containing closely related M proteins. In the current study, we used the emm cluster typing system, in combination with computational structure-based peptide modeling, as a novel approach to the design of potentially broadly protective M protein-based vaccines. METHODS M protein sequences (AA 16-50) from the E4 cluster containing 17 emm types of GAS were analyzed using de novo 3-D structure prediction tools and the resulting structures subjected to chemical diversity analysis to identify sequences that were the most representative of the 3-D physicochemical properties of the M peptides in the cluster. Five peptides that spanned the range of physicochemical attributes of all 17 peptides were used to formulate synthetic and recombinant vaccines. Rabbit antisera were assayed for antibodies that cross-reacted with E4 peptides and whole bacteria by ELISA and for bactericidal activity against all E4GAS. RESULTS The synthetic vaccine rabbit antisera reacted with all 17 E4M peptides and demonstrated bactericidal activity against 15/17 E4GAS. A recombinant hybrid vaccine containing the same E4 peptides also elicited antibodies that cross-reacted with all E4M peptides. CONCLUSIONS Comprehensive studies using structure-based design may result in a broadly protective M peptide vaccine that will elicit cluster-specific and emm type-specific antibody responses against the majority of clinically relevant emm types of GAS.
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Affiliation(s)
- James B Dale
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States; Department of Veterans Affairs Medical Center, Memphis, TN, United States.
| | - Pierre R Smeesters
- Department of Pediatrics, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium; Molecular Bacteriology Laboratory, Université Libre de Bruxelles, Brussels, Belgium; Group A Streptococcus Research Group, Murdoch Childrens Research Institute, Melbourne, Australia; Centre for International Child Health, University of Melbourne, Melbourne, Australia
| | - Harry S Courtney
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Thomas A Penfound
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Claudia M Hohn
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Oak Ridge, TN, United States; University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Jerome Y Baudry
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Oak Ridge, TN, United States; University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
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Daidone I, Zanetti-Polzi L, Thukral L, Alekozai EM, Amadei A. Theoretical-computational characterization of the temperature-dependent folding thermodynamics of a β-hairpin peptide. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Jas GS, Hegefeld WA, Middaugh CR, Johnson CK, Kuczera K. Detailed microscopic unfolding pathways of an α-helix and a β-hairpin: direct observation and molecular dynamics. J Phys Chem B 2014; 118:7233-46. [PMID: 24897620 DOI: 10.1021/jp500955z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We present a combined experimental and computational study of unfolding pathways of a model 21-residue α-helical heteropeptide (W1H5-21) and a 16-residue β-hairpin (GB41-56). Experimentally, we measured fluorescence energy transfer efficiency as a function of temperature, employing natural tryptophans as donors and dansylated lysines as acceptors. Secondary structural analysis was performed with circular dichroism and Fourier transform infrared spectroscopy. Our studies present markedly different unfolding pathways of the two elementary secondary structural elements. During thermal denaturation, the helical peptide exhibits an initial decrease in length, followed by an increase, while the hairpin undergoes a systematic increase in length. In the complementary computational part of the project, we performed microsecond length replica-exchange molecular dynamics simulations of the peptides in explicit solvent, yielding a detailed microscopic picture of the unfolding processes. For the α-helical peptide, we found a large heterogeneous population of intermediates that are primarily frayed single helices or helix-turn-helix motifs. Unfolding starts at the termini and proceeds through a stable helical region in the interior of the peptide but shifted off-center toward the C-terminus. The simulations explain the experimentally observed non-monotonic variation of helix length with temperature as due primarily to the presence of frayed-end single-helix intermediate structures. For the β-hairpin peptide, our simulations indicate that folding is initiated at the turn, followed by formation of the hairpin in zipper-like fashion, with Cα···Cα contacts propagating from the turn to termini and hairpin hydrogen bonds forming in parallel with these contacts. In the early stages of hairpin formation, the hydrophobic side-chain contacts are only partly populated. Intermediate structures with low numbers of β-hairpin hydrogen bonds have very low populations. This is in accord with the "broken zipper" model of Scheraga. The monotonic increase in length with temperature may be explained by the zipper-like breaking of the hairpin hydrogen bonds and backbone contacts.
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Affiliation(s)
- Gouri S Jas
- Department of Pharmaceutical Chemistry, University of Kansas , Lawrence, Kansas 66047, United States
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Copper-induced structural propensities of the amyloidogenic region of human prion protein. J Biol Inorg Chem 2014; 19:635-45. [DOI: 10.1007/s00775-014-1132-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 04/02/2014] [Indexed: 12/15/2022]
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Jas GS, Middaugh CR, Kuczera K. Non-exponential kinetics and a complete folding pathway of an α-helical heteropeptide: direct observation and comprehensive molecular dynamics. J Phys Chem B 2013; 118:639-47. [PMID: 24341828 DOI: 10.1021/jp410934g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have performed a combined experimental and computational study of the folding of a 21-residue α-helix-forming heteropeptide (WH21). Temperature jump kinetics with improved dynamic range at several temperatures revealed non-exponential relaxation that could be well described with two time constants of 20 and 300 ns at 298 K. In the computational part, we performed multi-microsecond molecular dynamics simulations of WH21 in explicit water, using the AMBER03 and OPLS/AA potentials. The simulations were in good agreement with available experimental data on helix content and relaxation times. On the basis of 70 individual transitions, we identified the main pathways of helix unfolding. Three paths were found in both force fields, with unfolding progressing through (1) N-terminus, C-terminus, and center; (2) C-terminus, N-terminus, and center; and (3) C-terminus, center, and N-terminus. An additional fourth path starting in the central region and expanding to the termini was detected only with AMBER03. Intermediate structures sampled along the pathway included a central helix with frayed termini, an off-center helix, and a helical hairpin. The simulations suggest that the short relaxation should be assigned to partly cooperative fluctuations of several neighboring hydrogen bonds. Overall, by a combination of ultrafast kinetic measurements and detailed microscopic description through comprehensive molecular dynamics, we have obtained important new insights into the helix folding process.
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Affiliation(s)
- Gouri S Jas
- Department of Pharmaceutical Chemistry, The University of Kansas , Lawrence, Kansas 66047, United States
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Liu L, Cao Z. Turn-directed α-β conformational transition of α-syn12 peptide at different pH revealed by unbiased molecular dynamics simulations. Int J Mol Sci 2013; 14:10896-907. [PMID: 23708094 PMCID: PMC3709708 DOI: 10.3390/ijms140610896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/24/2013] [Accepted: 04/24/2013] [Indexed: 11/16/2022] Open
Abstract
The transition from α-helical to β-hairpin conformations of α-syn12 peptide is characterized here using long timescale, unbiased molecular dynamics (MD) simulations in explicit solvent models at physiological and acidic pH values. Four independent normal MD trajectories, each 2500 ns, are performed at 300 K using the GROMOS 43A1 force field and SPC water model. The most clustered structures at both pH values are β-hairpin but with different turns and hydrogen bonds. Turn9-6 and four hydrogen bonds (HB9-6, HB6-9, HB11-4 and HB4-11) are formed at physiological pH; turn8-5 and five hydrogen bonds (HB8-5, HB5-8, HB10-3, HB3-10 and HB12-1) are formed at acidic pH. A common folding mechanism is observed: the formation of the turn is always before the formation of the hydrogen bonds, which means the turn is always found to be the major determinant in initiating the transition process. Furthermore, two transition paths are observed at physiological pH. One of the transition paths tends to form the most-clustered turn and improper hydrogen bonds at the beginning, and then form the most-clustered hydrogen bonds. Another transition path tends to form the most-clustered turn, and turn5-2 firstly, followed by the formation of part hydrogen bonds, then turn5-2 is extended and more hydrogen bonds are formed. The transition path at acidic pH is as the same as the first path described at physiological pH.
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Affiliation(s)
- Lei Liu
- Department of Computer Science and Technology, Dezhou University, Dezhou 253023, China; E-Mail:
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou 253023, China
| | - Zanxia Cao
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou 253023, China
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-534-8985879; Fax: +86-534-8985884
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