1
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Hossain M, Huda N, Bhuyan AK. A three-state mechanism for trifluoroethanol denaturation of an intrinsically disordered protein (IDP). J Biochem 2023; 174:519-531. [PMID: 37709541 DOI: 10.1093/jb/mvad067] [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: 04/27/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/16/2023] Open
Abstract
Relating the amino acid composition and sequence to chain folding and binding preferences of intrinsically disordered proteins (IDPs) has emerged as a huge challenge. While globular proteins have respective 3D structures that are unique to their individual functions, IDPs violate this structure-function paradigm because rather than having a well-defined structure an ensemble of rapidly interconverting disordered structures characterize an IDP. This work measures 2,2,2-trifluoroethanol (TFE)-induced equilibrium transitions of an IDP called AtPP16-1 (Arabidopsis thaliana phloem protein type 16-1) by using fluorescence, circular dichroism, infrared and nuclear magnetic resonance (NMR) methods at pH 4, 298 K. Low TFE reversibly removes the tertiary structure to produce an ensemble of obligate intermediate ($\mathrm{I}$) retaining the native-state ($\mathrm{N}$) secondary structure. The intermediate $\mathrm{I}$ is preceded by a non-obligate tryptophan-specific intermediate ${\mathrm{I}}_{\mathrm{w}}$ whose population is detectable for AtPP16-1 specifically. Accumulation of such non-obligate intermediates is discriminated according to the sequence composition of the protein. In all cases, however, a tertiary structure-unfolded general obligate intermediate $\mathrm{I}$ is indispensable. The $\mathrm{I}$ ensemble has higher helical propensity conducive to the acquisition of an exceedingly large level of α-helices by a reversible denaturation transition of $\mathrm{I}$ to the denatured state $\mathrm{D}$ as the TFE level is increased. Strikingly, it is the same $\mathrm{N}\rightleftharpoons \mathrm{I}\rightleftharpoons \mathrm{D}$ scheme typifying the TFE transitions of globular proteins. The high-energy state $\mathrm{I}$ characterized by increased helical propensity is called a universal intermediate encountered in both genera of globular and disordered proteins. Neither $\mathrm{I}$ nor $\mathrm{D}$ strictly show molten globule (MG)-like properties, dismissing the belief that TFE promotes MGs.
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Affiliation(s)
- Mujahid Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Noorul Huda
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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2
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Hasan MM, Polino AJ, Mukherjee S, Vaupel B, Goldberg DE. The mature N-termini of Plasmodium effector proteins confer specificity of export. mBio 2023; 14:e0121523. [PMID: 37646514 PMCID: PMC10653839 DOI: 10.1128/mbio.01215-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Malaria parasites export hundreds of proteins to the cytoplasm of the host red blood cells for their survival. A five amino acid sequence, called the PEXEL motif, is conserved among many exported proteins and is thought to be a signal for export. However, the motif is cleaved inside the endoplasmic reticulum of the parasite, and mature proteins starting from the fourth PEXEL residue travel to the parasite periphery for export. We showed that the PEXEL motif is dispensable for export as long as identical mature proteins can be efficiently produced via alternative means in the ER. We also showed that the exported and non-exported proteins are differentiated at the parasite periphery based on their mature N-termini; however, any discernible export signal within that region remained cryptic. Our study resolves a longstanding paradox in PEXEL protein trafficking.
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Affiliation(s)
- Muhammad M. Hasan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Alexander J. Polino
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sumit Mukherjee
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Barbara Vaupel
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daniel E. Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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3
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Rothfuss MT, Becht DC, Zeng B, McClelland LJ, Yates-Hansen C, Bowler BE. High-Accuracy Prediction of Stabilizing Surface Mutations to the Three-Helix Bundle, UBA(1), with EmCAST. J Am Chem Soc 2023; 145:22979-22992. [PMID: 37815921 PMCID: PMC10626973 DOI: 10.1021/jacs.3c04966] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
The accurate modeling of energetic contributions to protein structure is a fundamental challenge in computational approaches to protein analysis and design. We describe a general computational method, EmCAST (empirical Cα stabilization), to score and optimize the sequence to the structure in proteins. The method relies on an empirical potential derived from the database of the Cα dihedral angle preferences for all possible four-residue sequences, using the data available in the Protein Data Bank. Our method produces stability predictions that naturally correlate one-to-one with the experimental results for solvent-exposed mutation sites. EmCAST predicted four mutations that increased the stability of a three-helix bundle, UBA(1), from 2.4 to 4.8 kcal/mol by optimizing residues in both helices and turns. For a set of eight variants, the predicted and experimental stabilizations correlate very well (R2 = 0.97) with a slope near 1 and with a 0.16 kcal/mol standard error for EmCAST predictions. Tests against literature data for the stability effects of surface-exposed mutations show that EmCAST outperforms the existing stability prediction methods. UBA(1) variants were crystallized to verify and analyze their structures at an atomic resolution. Thermodynamic and kinetic folding experiments were performed to determine the magnitude and mechanism of stabilization. Our method has the potential to enable the rapid, rational optimization of natural proteins, expand the analysis of the sequence/structure relationship, and supplement the existing protein design strategies.
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Affiliation(s)
- Michael T. Rothfuss
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Dustin C. Becht
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Baisen Zeng
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Levi J. McClelland
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, United States
| | - Cindee Yates-Hansen
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, United States
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
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4
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Cheng G, Wang P, Liu H, Zhang D. A study of ab initio folding of chignolins using replica-exchange molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:23658-23666. [PMID: 37609919 DOI: 10.1039/d3cp03070a] [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: 08/24/2023]
Abstract
More and more studies have confirmed the importance of polarization effects in hydrogen bonding interactions in protein folding simulations. In this paper, a recently developed charge update scheme termed polarized structure-specific backbone charge (PSBC) model was applied to the folding of 10-residue chignolin. A comparison between simulations performed using PSBC and a nonpolarizable (AMBER99SB) force field demonstrably showed the importance of the electrostatic polarization effect in the folding of the short β-hairpin peptide by a series of analyses such as DSSP, free-energy landscape, hydrogen bond occupancy, and melting curve. The PSBC model was further validated by folding two other chignolin variants.
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Affiliation(s)
- Guojie Cheng
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, P. R. China.
| | - Panpan Wang
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, P. R. China.
| | - Huihui Liu
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, P. R. China.
| | - Dawei Zhang
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang 471023, P. R. China.
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5
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Length matters: Functional flip of the short TatA transmembrane helix. Biophys J 2022:S0006-3495(22)03926-1. [PMID: 36523158 DOI: 10.1016/j.bpj.2022.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The twin arginine translocase (Tat) exports folded proteins across bacterial membranes. The putative pore-forming or membrane-weakening component (TatAd in B. subtilis) is anchored to the lipid bilayer via an unusually short transmembrane α-helix (TMH), with less than 16 residues. Its tilt angle in different membranes was analyzed under hydrophobic mismatch conditions, using synchrotron radiation circular dichroism and solid-state NMR. Positive mismatch (introduced either by reconstitution in short-chain lipids or by extending the hydrophobic TMH length) increased the helix tilt of the TMH as expected. Negative mismatch (introduced either by reconstitution in long-chain lipids or by shortening the TMH), on the other hand, led to protein aggregation. These data suggest that the TMH of TatA is just about long enough for stable membrane insertion. At the same time, its short length is a crucial factor for successful translocation, as demonstrated here in native membrane vesicles using an in vitro translocation assay. Furthermore, when reconstituted in model membranes with negative spontaneous curvature, the TMH was found to be aligned parallel to the membrane surface. This intrinsic ability of TatA to flip out of the membrane core thus seems to play a key role in its membrane-destabilizing effect during Tat-dependent translocation.
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6
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Hossain M, Huda N, Bhuyan AK. A surprisingly simple three-state generic process for reversible protein denaturation by trifluoroethanol. Biophys Chem 2022; 291:106895. [PMID: 36182744 DOI: 10.1016/j.bpc.2022.106895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 12/30/2022]
Abstract
Despite the rich knowledge of the influence of 2,2,2-trifluoroethanol (TFE) on the structure and conformation of peptides and proteins, the mode(s) of TFE-protein interactions and the mechanism by which TFE reversibly denatures a globular protein remain elusive. This study systematically examines TFE-induced equilibrium transition curves for six paradigmatic globular proteins by using basic fluorescence and circular dichroism measurements under neutral pH conditions. The results are remarkably simple. Low TFE invariably unfolds the tertiary structure of all proteins to produce the obligate intermediate (I) which retains nearly all of native-state secondary structure, but enables the formation of extra α-helices as the level of TFE is raised higher. Inspection of the transitions at once reveals that the tertiary structure unfolding is always a distinct process, necessitating the inclusion of at least one obligate intermediate in the TFE-induced protein denaturation. It appears that the intermediate in the minimal unfolding mechanism N⇌I⇌D somehow acquires higher α-helical propensity to generate α-helices in excess of that in the native state to produce the denatured state (D), also called the TFE state. The low TFE-populated intermediate I may be called a universal intermediate by virtue of its α-helical propensity. Contrary to many earlier suggestions, this study dismisses molten globule (MG)-like attribute of I or D.
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Affiliation(s)
- Mujahid Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Noorul Huda
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
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7
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Pereira AF, Piccoli V, Martínez L. Trifluoroethanol direct interactions with protein backbones destabilize α-helices. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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8
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Kumar S, Venkatesha MA, Balaram P. Mechanistic Investigations on N-C α Bond Cleavages in Dibasic Peptides Containing Internal Lys and Arg Residues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1598-1606. [PMID: 35880778 DOI: 10.1021/jasms.2c00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The model nonapeptide AAARAAKAG* (* indicates amide) is used to explore N-Cα bond fragmentation under CID-MS conditions. Neighboring group participation and the effect of positioning of Lys and Arg residues on N-Cα bond cleavage is established using a library of synthetic peptide analogues. The importance of the Arg residue at position 4 and the i to i+3 spacing between Arg and Lys residues in determining the formation of the N-Cα bond cleaved product ions (cn) is demonstrated by a comparative MS study of positional variants in analogue peptides. The effect of shortening of the Lys side chain has been established using ornithine (Orn) and diaminobutyric acid (Dab) analogues. The involvement of the Lys residue in mediating the N-Cα bond cleavage is further probed using Nε-dimethyl and isotopically labeled 15Nα, ε lysine residues. MSn experiments reveal that the c6 ion originates from a doubly charged dehydrated b8 ion [b8-18]2+. The mechanism of this unusual fragmentation process has been probed by using position 8 analogues (Gly, Ala, and Aib). A plausible mechanism is proposed for the origin of the c6 ion, which involves C-terminus lactam formation followed by transannular cyclization and dehydration. The results presented in this study highlight the role of reactive side chain functionalities in promoting noncanonical fragmentation pathways.
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Affiliation(s)
- Sanjeev Kumar
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - M Achanna Venkatesha
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Padmanabhan Balaram
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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9
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Whisenant J, Burgess K. Synthetic helical peptide capping strategies. Chem Soc Rev 2022; 51:5795-5804. [PMID: 35786712 DOI: 10.1039/d1cs01175h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Relatively small mimics of interface secondary structures can be used to disrupt protein-protein interactions (PPIs). This strategy is valuable because many PPIs are pivotal in cell biology and contemporary medicinal chemistry. Small peptides tend to have random coil conformations in solution, so the entropy costs are high for them to order into states binding protein receptors. Consequently, peptides constrained in conformations resembling interface secondary structures are favored for enhanced affinities to PPI components. Helices are commonly found at PPI interfaces. The two general strategies that have emerged for imposing helical constraints in probes, capping and stapling, are often confused because both involve formation of macrocyclic rings. This review considers parameters that distinguish capping from stapling. Capping motifs terminate helices and project the adjacent peptide units in non-helical orientations, but stapling enforces helical motifs in ways that enable adjacent peptide fragments to extend helices. There is no evidence that stapling is more effective than capping for helix mimicry, but stapling is used more frequently. This imbalance may be because no strategies have emerged for synthetic C-capping with compact unit; if convenient and effective C-capping strategies were available then capping strategies should be more widely used.
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Affiliation(s)
- Jonathan Whisenant
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, USA.
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, Texas 77842, USA.
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10
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Banerjee R, Sheet T, Banerjee S, Biondi B, Formaggio F, Toniolo C, Peggion C. C α-Methyl-l-valine: A Preferential Choice over α-Aminoisobutyric Acid for Designing Right-Handed α-Helical Scaffolds. Biochemistry 2021; 60:2704-2714. [PMID: 34463474 DOI: 10.1021/acs.biochem.1c00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In synthetic peptides containing Gly and coded α-amino acids, one of the most common practices to enhance their helical extent is to incorporate a large number of l-Ala residues along with noncoded, strongly foldameric α-aminoisobutyric acid (Aib) units. Earlier studies have established that Aib-based peptides, with propensity for both the 310- and α-helices, have a tendency to form ordered three-dimensional structure that is much stronger than that exhibited by their l-Ala rich counterparts. However, the achiral nature of Aib induces an inherent, equal preference for the right- and left-handed helical conformations as found in Aib homopeptide stretches. This property poses challenges in the analysis of a model peptide helical conformation based on chirospectroscopic techniques like electronic circular dichroism (ECD), a very important tool for assigning secondary structures. To overcome such ambiguity, we have synthesized and investigated a thermally stable 14-mer peptide in which each of the Aib residues of our previously designed and reported analogue ABGY (where B stands for Aib) is replaced by Cα-methyl-l-valine (L-AMV). Analysis of the results described here from complementary ECD and 1H nuclear magnetic resonance spectroscopic techniques in a variety of environments firmly establishes that the L-AMV-containing peptide exhibits a significantly stronger preference compared to that of its Aib parent in terms of conferring α-helical character. Furthermore, being a chiral α-amino acid, L-AMV shows an intrinsic, extremely strong bias for a quite specific (right-handed) screw sense. These findings emphasize the relevance of L-AMV as a more appropriate unit for the design of right-handed α-helical peptide models that may be utilized as conformationally constrained scaffolds.
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Affiliation(s)
| | | | | | - Barbara Biondi
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
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11
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Bastida A, Zúñiga J, Requena A, Miguel B, Cerezo J. On the Role of Entropy in the Stabilization of α-Helices. J Chem Inf Model 2020; 60:6523-6531. [PMID: 33280379 DOI: 10.1021/acs.jcim.0c01177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein folding evolves by exploring the conformational space with a subtle balance between enthalpy and entropy changes which eventually leads to a decrease of free energy upon reaching the folded structure. A complete understanding of this process requires, therefore, a deep insight into both contributions to free energy. In this work, we clarify the role of entropy in favoring the stabilization of folded structures in polyalanine peptides with up to 12 residues. We use a novel method referred to as K2V that allows us to obtain the potential-energy landscapes in terms of residue conformations extracted from molecular dynamics simulations at conformational equilibrium and yields folding thermodynamic magnitudes, which are in agreement with the experimental data available. Our results demonstrate that the folded structures of the larger polyalanine chains are stabilized with respect to the folded structures of the shorter chains by both an energetic contribution coming from the formation of the intramolecular hydrogen bonds and an entropic contribution coming from an increase of the entropy of the solvent with approximate weights of 60 and 40%, respectively, thus unveiling a key piece in the puzzle of protein folding. In addition, the ability of the K2V method to provide the enthalpic and entropic contributions for individual residues along the peptide chain makes it clear that the energetic and entropic stabilizations are basically governed by the nearest neighbor residue conformations, with the folding propensity being rationalized in terms of triads of residues.
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Affiliation(s)
- Adolfo Bastida
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - José Zúñiga
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Alberto Requena
- Departamento de Química Física, Universidad de Murcia, 30100 Murcia, Spain
| | - Beatriz Miguel
- Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena, 30203 Cartagena, Spain
| | - Javier Cerezo
- Departamento de Química, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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12
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Yan X, Chu Y, Liu B, Ru G, Di Y, Feng J. Dynamic mechanism of halide salts on the phase transition of protein models, poly(N-isopropylacrylamide) and poly(N,N-diethylacrylamide). Phys Chem Chem Phys 2020; 22:12644-12650. [PMID: 32458929 DOI: 10.1039/d0cp01366h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The effects of salts on protein systems are not yet fully understood. We investigated the ionic dynamics of three halide salts (NaI, NaBr, and NaCl) with two protein models, namely poly(N-isopropylacrylamide) (PNIPAM) and poly(N,N-diethylacrylamide) (PDEA), using multinuclear NMR, dispersion corrected density functional theory (DFT-D) calculations and dynamic light scattering (DLS) methods. The variation in ionic line-widths and chemical shifts induced by the polymers clearly illustrates that anions rather than cations interact directly with the polymers. From the variable temperature measurements of the NMR transverse relaxation rates of anions, which characterize the polymer-anion interaction intensities, the evolution behaviors of Cl-/Br-/I- during phase transitions are similar in each polymer system but differ between the two polymer systems. The NMR transverse relaxation rates of anions change synchronously with the phase transition of PNIPAM upon heating, but they drop rapidly and vanish about 3-4.5 °C before the phase transition of PDEA. By combining the DFT-D and DLS data, the relaxation results imply that anions escape from the interacting sites with PDEA prior to full polymer dehydration or collapse, which can be attributed to the lack of anion-NH interactions. The different dynamic evolutions of the anions in the PNIPAM and PDEA systems give us an important clue for understanding the micro-mechanism of protein folding in a complex salt aqueous solvent.
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Affiliation(s)
- Xiaoshuang Yan
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China.
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13
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Tian C, Kasavajhala K, Belfon KAA, Raguette L, Huang H, Migues AN, Bickel J, Wang Y, Pincay J, Wu Q, Simmerling C. ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution. J Chem Theory Comput 2019; 16:528-552. [PMID: 31714766 DOI: 10.1021/acs.jctc.9b00591] [Citation(s) in RCA: 852] [Impact Index Per Article: 170.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a set of functions with adjustable parameters to compute the potential energies from atomic positions. However, the overall quality of the FF, such as our previously published ff99SB and ff14SB, can be limited by assumptions that were made years ago. In the updated model presented here (ff19SB), we have significantly improved the backbone profiles for all 20 amino acids. We fit coupled φ/ψ parameters using 2D φ/ψ conformational scans for multiple amino acids, using as reference data the entire 2D quantum mechanics (QM) energy surface. We address the polarization inconsistency during dihedral parameter fitting by using both QM and MM in aqueous solution. Finally, we examine possible dependency of the backbone fitting on side chain rotamer. To extensively validate ff19SB parameters, and to compare to results using other Amber models, we have performed a total of ∼5 ms MD simulations in explicit solvent. Our results show that after amino-acid-specific training against QM data with solvent polarization, ff19SB not only reproduces the differences in amino-acid-specific Protein Data Bank (PDB) Ramachandran maps better but also shows significantly improved capability to differentiate amino-acid-dependent properties such as helical propensities. We also conclude that an inherent underestimation of helicity is present in ff14SB, which is (inexactly) compensated for by an increase in helical content driven by the TIP3P bias toward overly compact structures. In summary, ff19SB, when combined with a more accurate water model such as OPC, should have better predictive power for modeling sequence-specific behavior, protein mutations, and also rational protein design. Of the explicit water models tested here, we recommend use of OPC with ff19SB.
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Affiliation(s)
- Chuan Tian
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Koushik Kasavajhala
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Kellon A A Belfon
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Lauren Raguette
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - He Huang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Angela N Migues
- Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - John Bickel
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Yuzhang Wang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Jorge Pincay
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Qin Wu
- Center for Functional Nanomaterials , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Carlos Simmerling
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
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14
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Vincenzi M, Mercurio FA, Leone M. About TFE: Old and New Findings. Curr Protein Pept Sci 2019; 20:425-451. [PMID: 30767740 DOI: 10.2174/1389203720666190214152439] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 01/28/2023]
Abstract
The fluorinated alcohol 2,2,2-Trifluoroethanol (TFE) has been implemented for many decades now in conformational studies of proteins and peptides. In peptides, which are often disordered in aqueous solutions, TFE acts as secondary structure stabilizer and primarily induces an α -helical conformation. The exact mechanism through which TFE plays its stabilizing roles is still debated and direct and indirect routes, relying either on straight interaction between TFE and molecules or indirect pathways based on perturbation of solvation sphere, have been proposed. Another still unanswered question is the capacity of TFE to favor in peptides a bioactive or a native-like conformation rather than simply stimulate the raise of secondary structure elements that reflect only the inherent propensity of a specific amino-acid sequence. In protein studies, TFE destroys unique protein tertiary structure and often leads to the formation of non-native secondary structure elements, but, interestingly, gives some hints about early folding intermediates. In this review, we will summarize proposed mechanisms of TFE actions. We will also describe several examples, in which TFE has been successfully used to reveal structural properties of different molecular systems, including antimicrobial and aggregation-prone peptides, as well as globular folded and intrinsically disordered proteins.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia A Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
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15
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Zhang D, Lazim R, Yip YM. Incorporating Polarizability of Backbone Hydrogen Bonds Improved Folding of Short α-Helical Peptides. Biophys J 2019; 117:2079-2086. [PMID: 31685242 DOI: 10.1016/j.bpj.2019.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/02/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022] Open
Abstract
Reliability of force fields is an essential aspect of protein-folding simulation. In this work, we introduced a newly developed on-the-fly charge-updating scheme called the polarized structure-specific backbone charge (PSBC) model. The PSBC model was designed with the purpose of building the polarizability of backbone hydrogen bonds into the force field by updating the partial charges of backbone hydrogen-bond donor and acceptor atoms during folding simulation. This implementation was intended to mimic the heterogeneity of the protein surrounding during folding. Multiple single-trajectory molecular dynamics simulations were performed to fold a polyalanine peptide, namely ER (Ac-A(EAAAR)3A-NH2), using both polarizable (PSBC) and nonpolarizable (Amber03) force fields. Through the PSBC model, ER was folded into a helical peptide with helix content that agrees well with experiments. Comparison between simulations performed using the aforementioned force fields demonstrably showed the importance of electrostatic polarization effect in the folding of the short α-helical peptide. The PSBC model was further validated by folding two other short peptides with different helicities.
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Affiliation(s)
- Dawei Zhang
- School of Physics and Engineering, Henan University of Science and Technology, Luoyang, P. R. China; Henan Key Laboratory of Photoelectric Energy Storage Materials and Applications, Henan University of Science and Technology, Luoyang, P. R. China.
| | - Raudah Lazim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Yew Mun Yip
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
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16
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Sun Z, Wang X. Thermodynamics of Helix formation in small peptides of varying lengthin vacuo, implicit solvent and explicit solvent: Comparison between AMBER force fields. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Helix formation is of great significance in protein folding. The helix-forming tendencies of amino acids are accumulated along the sequence to determine the helix-forming tendency of peptides. Computer simulation can be used to model this process in atomic details and give structural insights. In the current work, we employ equilibrate-state free energy simulation to systematically study the folding/unfolding thermodynamics of a series of mutated peptides. Two AMBER force fields including AMBER99SB and AMBER14SB are compared. The new 14SB force field uses refitted torsion parameters compared with 99SB and they share the same atomic charge scheme. We find that in vacuo the helix formation is mutation dependent, which reflects the different helix propensities of different amino acids. In general, there are helix formers, helix indifferent groups and helix breakers. The helical structure becomes more favored when the length of the sequence becomes longer, which arises from the formation of additional backbone hydrogen bonds in the lengthened sequence. Therefore, the helix indifferent groups and helix breakers will become helix formers in long sequences. Also, protonation-dependent helix formation is observed for ionizable groups. In 14SB, the helical structures are more stable than in 99SB and differences can be observed in their grouping schemes, especially in the helix indifferent group. In solvents, all mutations are helix indifferent due to protein–solvent interactions. The decrease in the number of backbone hydrogen bonds is the same with the increase in the number of protein–water hydrogen bonds. The 14SB in explicit solvent is able to capture the free energy minima in the helical state while 14SB in implicit solvent, 99SB in explicit solvent and 99SB in implicit solvent cannot. The helix propensities calculated under 14SB agree with the corresponding experimental values, while the 99SB results obviously deviate from the references. Hence, implicit solvent models are unable to correctly describe the thermodynamics even for the simple helix formation in isolated peptides. Well-developed force fields and explicit solvents are needed to correctly describe the protein dynamics. Aside from the free energy, differences in conformational ensemble under different force fields in different solvent models are observed. The numbers of hydrogen bonds formed under different force fields agree and they are mostly determined by the solvent model.
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Affiliation(s)
- Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich 52425, Germany
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, P. R. China
- Institute of Computational Science, Universitàdella Svizzeraitaliana (USI), Via Giuseppe Buffi 13, CH-6900 Lugano, Ticino, Switzerland
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17
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Conformational Change of Amyloid-β 40 in Association with Binding to GM1-Glycan Cluster. Sci Rep 2019; 9:6853. [PMID: 31048748 PMCID: PMC6497634 DOI: 10.1038/s41598-019-43117-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/15/2019] [Indexed: 12/22/2022] Open
Abstract
Aggregates of amyloid-β (Aβ) peptide are well known to be the causative substance of Alzheimer's disease (AD). Recent studies showed that monosialotetrahexosylganglioside (GM1) clusters induce the pathological aggregation of Aβ peptide responsible for the onset and development of AD. However, the effect of GM1-glycan cluster on Aβ conformations has yet to be clarified. Interactions between Aβ peptide and GM1-glycan cluster is important for the earliest stage of the toxic aggregation on GM1 cluster. Here, we performed all-atom molecular dynamics (MD) simulations of Aβ40 on a recently developed artificial GM1-glycan cluster. The artificial GM1-glycan cluster facilitates the characterization of interactions between Aβ40 and multiple GM1-glycans. We succeeded in observing the binding of Aβ40 to the GM1-glycan cluster in all of our MD simulations. Results obtained from these MD simulations indicate the importance of HHQ (13-15) segment of Aβ40 for the GM1-glycan cluster recognition. This result is consistent with previous experimental studies regarding the glycan recognition of Aβ peptide. The recognition mechanism of HHQ (13-15) segment is mainly explained by non-specific stacking interactions between side-chains of histidine and rings of sugar residues, in which the HHQ regime forms coil and bend structures. Moreover, we found that Aβ40 exhibits helix structures at C-terminal side on the GM1-glycan cluster. The helix formation is the initial stage of the pathological aggregation at ceramide moieties of GM1 cluster. The binding of Lys28 to Neu triggers the helix formation at C-terminus side because the formation of a salt bridge between Lys28 and Neu leads to change of intrachain interactions of Aβ40. Our findings suggest that the pathological helix formation of Aβ40 is initiated at GM1-glycan moieties rather than lipid ceramide moieties.
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18
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Mariño L, Casasnovas R, Ramis R, Vilanova B, Ortega-Castro J, Frau J, Adrover M. Does glycation really distort the peptide α-helicity? Int J Biol Macromol 2019; 129:254-266. [DOI: 10.1016/j.ijbiomac.2019.01.213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/23/2018] [Accepted: 01/31/2019] [Indexed: 01/19/2023]
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19
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Dedkova LM, Hecht SM. Expanding the Scope of Protein Synthesis Using Modified Ribosomes. J Am Chem Soc 2019; 141:6430-6447. [PMID: 30901982 DOI: 10.1021/jacs.9b02109] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The ribosome produces all of the proteins and many of the peptides present in cells. As a macromolecular complex composed of both RNAs and proteins, it employs a constituent RNA to catalyze the formation of peptide bonds rapidly and with high fidelity. Thus, the ribosome can be argued to represent the key link between the RNA World, in which RNAs were the primary catalysts, and present biological systems in which protein catalysts predominate. In spite of the well-known phylogenetic conservation of rRNAs through evolutionary history, rRNAs can be altered readily when placed under suitable pressure, e.g. in the presence of antibiotics which bind to functionally critical regions of rRNAs. While the structures of rRNAs have been altered intentionally for decades to enable the study of their role(s) in the mechanism of peptide bond formation, it is remarkable that the purposeful alteration of rRNA structure to enable the elaboration of proteins and peptides containing noncanonical amino acids has occurred only recently. In this Perspective, we summarize the history of rRNA modifications, and demonstrate how the intentional modification of 23S rRNA in regions critical for peptide bond formation now enables the direct ribosomal incorporation of d-amino acids, β-amino acids, dipeptides and dipeptidomimetic analogues of the normal proteinogenic l-α-amino acids. While proteins containing metabolically important functional groups such as carbohydrates and phosphate groups are normally elaborated by the post-translational modification of nascent polypeptides, the use of modified ribosomes to produce such polymers directly is also discussed. Finally, we describe the elaboration of such modified proteins both in vitro and in bacterial cells, and suggest how such novel biomaterials may be exploited in future studies.
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Affiliation(s)
- Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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20
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Graham KA, Byrne A, Son R, Andersen NH. Reversing the typical pH stability profile of the Trp-cage. Biopolymers 2019; 110:e23260. [PMID: 30779444 DOI: 10.1002/bip.23260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/14/2018] [Accepted: 01/07/2019] [Indexed: 12/18/2022]
Abstract
The Trp-cage, an 18-20 residue miniprotein, has emerged as a primary test system for evaluating computational fold prediction and folding rate determination efforts. As it turns out, a number of stabilizing interactions in the Trp-cage folded state have a strong pH dependence; all prior Trp-cage mutants have been destabilized under carboxylate-protonating conditions. Notable among the pH dependent stabilizing interactions within the Trp-cage are: (1) an Asp as the helix N-cap, (2) an H-bonded Asp9/Arg16 salt bridge, (3) an interaction between the chain termini which are in close spatial proximity, and (4) additional side chain interactions with Asp9. In the present study, we have prepared Trp-cage species that are significantly more stable at pH 2.5 (rather than 7) and quantitated the contribution of each interaction listed above. The Trp-cage structure remains constant with the pH change. The study has also provided measures of the stabilizing contribution of indole ring shielding from surface exposure and the destabilizing effects of an ionized Asp at the C-terminus of an α-helix.
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Affiliation(s)
| | - Aimee Byrne
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Ruth Son
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, Washington
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21
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Wang J, Chen J, Li J, An L, Wang Y, Huang Q, Yao L. Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way. Proteins 2018; 86:684-692. [PMID: 29575221 DOI: 10.1002/prot.25495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 03/07/2018] [Accepted: 03/15/2018] [Indexed: 11/10/2022]
Abstract
A combined experimental and computational study is performed for arginine side chain stacking with the protein α-helix. Theremostability measurements of Aristaless homeodomain, a helical protein, suggest that mutating the arginine residue R106, R137 or R141, which has the guanidino side chain stacking with the peptide plane, to alanine, destabilizes the protein. The R-PP stacking has an energy of ∼0.2-0.4 kcal/mol. This stacking interaction mainly comes from dispersion and electrostatics, based on MP2 calculations with the energy decomposition analysis. The calculations also suggest that the stacking stabilizes 2 backbone-backbone h-bonds (i→i-4 and i-3→i-7) in a cooperative way. Desolvation and electrostatic polarization are responsible for cooperativity with the i→i-4 and i-3→i-7 h-bonds, respectively. This cooperativity is supported by a protein α-helices h-bond survey in the pdb databank where stacking shortens the corresponding h-bond distances.
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Affiliation(s)
- Jia Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Qingdao Institute of Bioenergy and Bioprocess Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingfei Chen
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Jingwen Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Qingdao Institute of Bioenergy and Bioprocess Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liaoyuan An
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Yefei Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Qingshan Huang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Lishan Yao
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
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22
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Leavens MJ, Cherney MM, Finnegan ML, Bowler BE. Probing Denatured State Conformational Bias in a Three-Helix Bundle, UBA(2), Using a Cytochrome c Fusion Protein. Biochemistry 2018; 57:1711-1721. [PMID: 29480716 DOI: 10.1021/acs.biochem.8b00015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previous work with the four-helix-bundle protein cytochrome c' from Rhodopseudomonas palustris using histidine-heme loop formation methods revealed fold-specific deviations from random coil behavior in its denatured state ensemble. To examine the generality of this finding, we extend this work to a three-helix-bundle polypeptide, the second ubiquitin-associated domain, UBA(2), of the human DNA excision repair protein. We use yeast iso-1-cytochrome c as a scaffold, fusing the UBA(2) domain at the N-terminus of iso-1-cytochrome c. We have engineered histidine into highly solvent accessible positions of UBA(2), creating six single histidine variants. Guanidine hydrochloride denaturation studies show that the UBA(2)-cytochrome c fusion protein unfolds in a three-state process with iso-1-cytochrome c unfolding first. Furthermore, engineered histidine residues in UBA(2) strongly destabilize the iso-1-cytochrome c domain. Equilibrium and kinetic histidine-heme loop formation measurements in the denatured state at 4 and 6 M guanidine hydrochloride show that loop stability decreases as the size of the histidine-heme loop increases, in accord with the Jacobson-Stockmayer equation. However, we observe that the His27-heme loop is both more stable than expected from the Jacobson-Stockmayer relationship and breaks more slowly than expected. These results show that the sequence near His27, which is in the reverse turn between helices 2 and 3 of UBA(2), is prone to persistent interactions in the denatured state. Therefore, consistent with our results for cytochrome c', this reverse turn sequence may help to establish the topology of this fold by biasing the conformational distribution of the denatured state.
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Affiliation(s)
- Moses J Leavens
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Melisa M Cherney
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Michaela L Finnegan
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
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23
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Xu X, Xiao X, Xu S, Liu H. Computational insights into the destabilization of α-helical conformations formed by leucine zipper peptides in response to temperature. Phys Chem Chem Phys 2018; 18:25465-25473. [PMID: 27722604 DOI: 10.1039/c6cp05145f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent experiments in our lab (Phys. Chem. Chem. Phys., 2016, 18, 10129-10137) suggested using leucine zipper peptides to enhance the thermosensitivity of liposomes. To understand the mechanisms of temperature-responsive control by the leucine zipper peptide in liposomes, we firstly performed quantum mechanics calculations and implicit-solvent replica exchange molecular dynamics simulations to study the thermo-stability of two leucine zipper peptides, CH3(CH2)4-CO-[VAQLEVK-VAQLESK-VSKLESK-VSSLESK] (termed the capped peptide) and A-[VAQLEVK-VAQLESK-VSKLESK-VSSLESK] (termed the ALA peptide). The analysis of dihedral angle principal components and protein secondary structures was conducted to determine the temperature-dependence conformation transition of the two peptides. Simulation results revealed that our computed transition temperature of the capped peptide is 319.1 K that accords with experimental measurement, 321.1 K. Later, explicit-solvent conventional molecular dynamics simulations were carried out to examine the process of folding and unfolding of the ALA and capped peptides complexed with a lipid bilayer and water in the vicinity of their transition temperatures. A further analysis of conformation and energy of the folded peptides showed that the increase of temperature gives rise to a notable decrease in the number of intra-chain hydrogen bonds and a significant increase in the potential energy of the peptides, thereby reducing the folding stability of the two peptides. As compared to the ALA peptide, a lower transition temperature caused by less intra-chain hydrogen bonds was observed in the capped peptide, which is closer to the temperature of tumor cells. This fact suggests that the capped peptide is more suitable to produce highly sensitive liposomes for the delivery of cancer drugs.
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Affiliation(s)
- Xiejun Xu
- State Key Laboratory of Chemical Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Xingqing Xiao
- Chemical and Biomolecular Engineering Department, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
| | - Shouhong Xu
- State Key Laboratory of Chemical Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Honglai Liu
- State Key Laboratory of Chemical Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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24
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Danielson TA, Bowler BE. Helical Propensity Affects the Conformational Properties of the Denatured State of Cytochrome c'. Biophys J 2018; 114:311-322. [PMID: 29401429 DOI: 10.1016/j.bpj.2017.11.3744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/18/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022] Open
Abstract
Changing the helical propensity of a polypeptide sequence might be expected to affect the conformational properties of the denatured state of a protein. To test this hypothesis, alanines at positions 83 and 87 near the center of helix 3 of cytochrome c' from Rhodopseudomonas palustris were mutated to serine to decrease the stability of this helix. A set of 13 single histidine variants in the A83S/A87S background were prepared to permit assessment of the conformational properties of the denatured state using histidine-loop formation in 3 M guanidine hydrochloride. The data are compared with previous histidine-heme loop formation data for wild-type cytochrome c'. As expected, destabilization of helix 3 decreases the global stabilities of the histidine variants in the A83S/A87S background relative to the wild-type background. Loop stability versus loop size data yields a scaling exponent of 2.1 ± 0.2, similar to the value of 2.3 ± 0.2 obtained for wild-type cytochrome c'. However, the stabilities of all histidine-heme loops, which contain the helix 3 sequence segment, are increased in the A83S/A87S background compared to the wild-type background. Rate constants for histidine-heme loop breakage are similar for the wild-type and A83S/A87S variants. However, for histidine-heme loops that contain the helix 3 sequence segment, the rate constants for loop formation increase in the A83S/A87S background compared to the wild-type background. Thus, residual helical structure appears to stiffen the polypeptide chain slowing loop formation in the denatured state. The implications of these results for protein folding mechanisms are discussed.
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Affiliation(s)
- Travis A Danielson
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana.
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25
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Danielson TA, Stine JM, Dar TA, Briknarova K, Bowler BE. Effect of an Imposed Contact on Secondary Structure in the Denatured State of Yeast Iso-1-cytochrome c. Biochemistry 2017; 56:6662-6676. [PMID: 29148740 DOI: 10.1021/acs.biochem.7b01002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is considerable evidence that long-range interactions stabilize residual protein structure under denaturing conditions. However, evaluation of the effect of a specific contact on structure in the denatured state has been difficult. Iso-1-cytochrome c variants with a Lys54 → His mutation form a particularly stable His-heme loop in the denatured state, suggestive of loop-induced residual structure. We have used multidimensional nuclear magnetic resonance methods to assign 1H and 15N backbone amide and 13C backbone and side chain chemical shifts in the denatured state of iso-1-cytochrome c carrying the Lys54 → His mutation in 3 and 6 M guanidine hydrochloride and at both pH 6.4, where the His54-heme loop is formed, and pH 3.6, where the His54-heme loop is broken. Using the secondary structure propensity score, with the 6 M guanidine hydrochloride chemical shift data as a random coil reference state for data collected in 3 M guanidine hydrochloride, we found residual helical structure in the denatured state for the 60s helix and the C-terminal helix, but not in the N-terminal helix in the presence or absence of the His54-heme loop. Non-native helical structure is observed in two regions that form Ω-loops in the native state. There is more residual helical structure in the C-terminal helix at pH 6.4 when the loop is formed. Loop formation also appears to stabilize helical structure near His54, consistent with induction of helical structure observed when His-heme bonds form in heme-peptide model systems. The results are discussed in the context of the folding mechanism of cytochrome c.
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Affiliation(s)
- Travis A Danielson
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Jessica M Stine
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Tanveer A Dar
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Klara Briknarova
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana , Missoula, Montana 59812, United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana , Missoula, Montana 59812, United States
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26
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Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics. Biophys J 2017; 110:2328-2341. [PMID: 27276251 DOI: 10.1016/j.bpj.2016.04.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/17/2016] [Accepted: 04/08/2016] [Indexed: 01/24/2023] Open
Abstract
Using a combination of ultraviolet circular dichroism, temperature-jump transient-infrared spectroscopy, and molecular dynamics simulations, we investigate the effect of salt bridges between different types of charged amino-acid residue pairs on α-helix folding. We determine the stability and the folding and unfolding rates of 12 alanine-based α-helical peptides, each of which has a nearly identical composition containing three pairs of positively and negatively charged residues (either Glu(-)/Arg(+), Asp(-)/Arg(+), or Glu(-)/Lys(+)). Within each set of peptides, the distance and order of the oppositely charged residues in the peptide sequence differ, such that they have different capabilities of forming salt bridges. Our results indicate that stabilizing salt bridges (in which the interacting residues are spaced and ordered such that they favor helix formation) speed up α-helix formation by up to 50% and slow down the unfolding of the α-helix, whereas salt bridges with an unfavorable geometry have the opposite effect. Comparing the peptides with different types of charge pairs, we observe that salt bridges between side chains of Glu(-) and Arg(+) are most favorable for the speed of folding, probably because of the larger conformational space of the salt-bridging Glu(-)/Arg(+) rotamer pairs compared to Asp(-)/Arg(+) and Glu(-)/Lys(+). We speculate that the observed impact of salt bridges on the folding kinetics might explain why some proteins contain salt bridges that do not stabilize the final, folded conformation.
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27
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Abdul Ghani NS, Karjiban RA, Basri M, Faujan NH, Lim WZ. Unveiling Amyloid-β1–42 Interaction with Zinc in Water and Mixed Hexafluoroisopropanol Solution in Alzheimer’s Disease. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-016-9570-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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28
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Doig AJ. Frozen, but no accident – why the 20 standard amino acids were selected. FEBS J 2017; 284:1296-1305. [DOI: 10.1111/febs.13982] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/23/2016] [Accepted: 12/02/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew J. Doig
- Department of Chemistry Manchester Institute of Biotechnology University of Manchester UK
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29
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Kusunoki H, Tanaka T, Kohno T, Kimura H, Hosoda K, Wakamatsu K, Hamaguchi I. Expression, purification and characterization of hepatitis B virus X protein BH3-like motif-linker-Bcl-x L fusion protein for structural studies. Biochem Biophys Rep 2016; 9:159-165. [PMID: 29114584 PMCID: PMC5632712 DOI: 10.1016/j.bbrep.2016.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/12/2016] [Accepted: 12/19/2016] [Indexed: 11/24/2022] Open
Abstract
Hepatitis B virus X protein (HBx) is a multifunctional protein that interacts directly with many host proteins. For example, HBx interacts with anti-apoptotic proteins, Bcl-2 and Bcl-xL, through its BH3-like motif, which leads to elevated cytosolic calcium levels, efficient viral DNA replication and the induction of apoptosis. To facilitate sample preparation and perform detailed structural characterization of the complex between HBx and Bcl-xL, we designed and purified a recombinant HBx BH3-like motif-linker-Bcl-xL fusion protein produced in E. coli. The fusion protein was characterized by size exclusion chromatography, circular dichroism and nuclear magnetic resonance experiments. Our results show that the fusion protein is a monomer in aqueous solution, forms a stable intramolecular complex, and likely retains the native conformation of the complex between Bcl-xL and the HBx BH3-like motif. Furthermore, the HBx BH3-like motif of the intramolecular complex forms an α-helix. These observations indicate that the fusion protein should facilitate structural studies aimed at understanding the interaction between HBx and Bcl-xL at the atomic level. Soluble HBx BH3-like motif-linker-Bcl-xL fusion protein was produced in E. coli. The fusion protein behaves as a monomer and forms a stable intramolecular complex. The HBx BH3-like motif of the fusion protein forms an α-helix. The fusion protein likely retains the native conformation of the complex.
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Affiliation(s)
- Hideki Kusunoki
- Department of Research on Blood and Biological Products, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Toshiyuki Tanaka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Toshiyuki Kohno
- Department of Biochemistry, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Kazuo Hosoda
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Kaori Wakamatsu
- Department of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Isao Hamaguchi
- Department of Research on Blood and Biological Products, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
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Anderson JM, Jurban B, Huggins KNL, Shcherbakov AA, Shu I, Kier B, Andersen NH. Nascent Hairpins in Proteins: Identifying Turn Loci and Quantitating Turn Contributions to Hairpin Stability. Biochemistry 2016; 55:5537-5553. [DOI: 10.1021/acs.biochem.6b00732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jordan M. Anderson
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Brice Jurban
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Kelly N. L. Huggins
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | | | - Irene Shu
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Brandon Kier
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Niels H. Andersen
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
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31
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Zhou Y, He L, Zhang W, Hu J, Shi Z. Populations of the Minor α-Conformation in AcGXGNH2 and the α-Helical Nucleation Propensities. Sci Rep 2016; 6:27197. [PMID: 27256621 PMCID: PMC4891685 DOI: 10.1038/srep27197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/16/2016] [Indexed: 01/25/2023] Open
Abstract
Intrinsic backbone conformational preferences of different amino acids are important for understanding the local structure of unfolded protein chains. Recent evidence suggests α-structure is relatively minor among three major backbone conformations for unfolded proteins. The α-helices are the dominant structures in many proteins. For these proteins, how could the α-structures occur from the least in unfolded to the most in folded states? Populations of the minor α-conformation in model peptides provide vital information. Reliable determination of populations of the α-conformers in these peptides that exist in multiple equilibriums of different conformations remains a challenge. Combined analyses on data from AcGXPNH2 and AcGXGNH2 peptides allow us to derive the populations of PII, β and α in AcGXGNH2. Our results show that on average residue X in AcGXGNH2 adopt PII, β, and α 44.7%, 44.5% and 10.8% of time, respectively. The contents of α-conformations for different amino acids define an α-helix nucleation propensity scale. With derived PII, β and α-contents, we can construct a free energy-conformation diagram on each AcGXGNH2 in aqueous solution for the three major backbone conformations. Our results would have broad implications on early-stage events of protein folding.
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Affiliation(s)
- Yanjun Zhou
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, P.R. China
| | - Liu He
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, P.R. China
| | - Wenwen Zhang
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, P.R. China
| | - Jingjing Hu
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, P.R. China
| | - Zhengshuang Shi
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, P.R. China
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32
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Dannenberg JJ. The importance of cooperative interactions and a solid-state paradigm to proteins: what Peptide chemists can learn from molecular crystals. ACTA ACUST UNITED AC 2016; 72:227-73. [PMID: 16581379 DOI: 10.1016/s0065-3233(05)72009-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Proteins and peptides in solution or in vivo share properties with both liquids and solids. More often than not, they are studied using the liquid paradigm rather than that of a solid. Studies of molecular crystals illustrate how the use of a solid paradigm may change the way that we consider these important molecules. Cooperative interactions, particularly those involving H-bonding, play much more important roles in the solid than in the liquid paradigms, as molecular crystals clearly illustrate. Using the solid rather than the liquid paradigm for proteins and peptides includes these cooperative interactions while application of the liquid paradigm tends to ignore or minimize them. Use of the solid paradigm has important implications for basic principles that are often implied about peptide and protein chemistry, such as the importance of entropy in protein folding and the nature of the hydrophobic effect. Understanding the folded states of peptides and proteins (especially alpha-helices) often requires the solid paradigm, whereas understanding unfolded states does not. Both theoretical and experimental studies of the energetics of protein and peptide folding require comparison to a suitable standard. Our perspective on these energetics depends on the reasonable choice of reference. The use of multiple reference states, particularly that of component amino acids in the gas phase, is proposed.
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Affiliation(s)
- J J Dannenberg
- Department of Chemistry, City University of New York, Hunter College and the Graduate School New York, New York 10021
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33
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Mauran L, Kauffmann B, Odaert B, Guichard G. Stabilization of an α-helix by short adjacent accessory foldamers. CR CHIM 2016. [DOI: 10.1016/j.crci.2015.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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34
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Fremaux J, Mauran L, Pulka-Ziach K, Kauffmann B, Odaert B, Guichard G. α-Peptide-Oligourea Chimeras: Stabilization of Short α-Helices by Non-Peptide Helical Foldamers. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500901] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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35
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Fremaux J, Mauran L, Pulka‐Ziach K, Kauffmann B, Odaert B, Guichard G. α‐Peptide–Oligourea Chimeras: Stabilization of Short α‐Helices by Non‐Peptide Helical Foldamers. Angew Chem Int Ed Engl 2015; 54:9816-20. [DOI: 10.1002/anie.201500901] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/23/2015] [Indexed: 01/27/2023]
Affiliation(s)
- Juliette Fremaux
- Univ. Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie et Biologie (IECB), 2 rue Robert Escarpit, 33607 Pessac (France)
- CNRS, CBMN, UMR 5248, 33600 Pessac (France)
- UREkA, Sarl, 2 rue Robert Escarpit, 33607 Pessac (France)
| | - Laura Mauran
- Univ. Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie et Biologie (IECB), 2 rue Robert Escarpit, 33607 Pessac (France)
- CNRS, CBMN, UMR 5248, 33600 Pessac (France)
- UREkA, Sarl, 2 rue Robert Escarpit, 33607 Pessac (France)
| | - Karolina Pulka‐Ziach
- Univ. Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie et Biologie (IECB), 2 rue Robert Escarpit, 33607 Pessac (France)
- CNRS, CBMN, UMR 5248, 33600 Pessac (France)
- Present address: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02‐093 Warsaw (Poland)
| | - Brice Kauffmann
- Univ. Bordeaux, IECB, UMS 3033/US 001, 2 rue Escarpit, 33607 Pessac (France)
- CNRS, IECB, UMS 3033, 33600 Pessac (France)
- INSERM, IECB, US 001, 33600 Pessac (France)
| | - Benoit Odaert
- CNRS, CBMN, UMR 5248, 33600 Pessac (France)
- Univ. Bordeaux, CBMN, UMR 5248, All. Geoffroy Saint‐Hilaire, 33600 Pessac (France)
| | - Gilles Guichard
- Univ. Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie et Biologie (IECB), 2 rue Robert Escarpit, 33607 Pessac (France)
- CNRS, CBMN, UMR 5248, 33600 Pessac (France)
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36
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Pavšič M, Ilc G, Vidmar T, Plavec J, Lenarčič B. The cytosolic tail of the tumor marker protein Trop2--a structural switch triggered by phosphorylation. Sci Rep 2015; 5:10324. [PMID: 25981199 PMCID: PMC4434849 DOI: 10.1038/srep10324] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/08/2015] [Indexed: 01/23/2023] Open
Abstract
Trop2 is a transmembrane signaling glycoprotein upregulated in stem and carcinoma cells. Proliferation-enhancing signaling involves regulated intramembrane proteolytic release of a short cytoplasmic fragment, which is later engaged in a cytosolic signaling complex. We propose that Trop2 function is modulated by phosphorylation of a specific serine residue within this cytosolic region (Ser303), and by proximity effects exerted on the cytosolic tail by Trop2 dimerization. Structural characterization of both the transmembrane (Trop2TM) and cytosolic regions (Trop2IC) support this hypothesis, and shows that the central region of Trop2IC forms an α-helix. Comparison of NMR structures of non-phosphorylated and phosphorylated forms suggest that phosphorylation of Trop2IC triggers salt bridge reshuffling, resulting in significant conformational changes including ordering of the C-terminal tail. In addition, we demonstrate that the cytosolic regions of two Trop2 subunits can be brought into close proximity via transmembrane part dimerization. Finally, we show that Ser303-phosphorylation significantly affects the structure and accessibility of functionally important regions of the cytosolic tail. These observed structural features of Trop2 at the membrane-cytosol interface could be important for regulation of Trop2 signaling activity.
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Affiliation(s)
- Miha Pavšič
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Gregor Ilc
- 1] Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia [2] EN-FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Tilen Vidmar
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Janez Plavec
- 1] Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia [2] Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia [3] EN-FIST Centre of Excellence, Dunajska 156, SI-1000 Ljubljana, Slovenia
| | - Brigita Lenarčič
- 1] Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia [2] J. Stefan Institute, Department of Biochemistry, Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia
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37
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Huang J, MacKerell AD. Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide. Biophys J 2015; 107:991-7. [PMID: 25140435 DOI: 10.1016/j.bpj.2014.06.038] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/19/2014] [Accepted: 06/24/2014] [Indexed: 11/27/2022] Open
Abstract
Cooperativity is a central feature in the formation of secondary structures in proteins. However, the driving forces behind this cooperativity are poorly understood. The present work shows that the cooperativity of helix formation in the acetyl-(AAQAA)3-NH2 peptide is significantly enhanced using an empirical force field that explicitly includes the treatment of electronic polarizability. Polarizable simulations yield helical content consistent with experimental measurements and indicate that the dependence of helical content on temperature is improved over additive models, though further sampling is required to fully validate this conclusion. Cooperativity is indicated by the peptide sampling either the coiled state or long helices with relatively low populations of short helices. The cooperativity is shown to be associated with enhanced dipole moments of the peptide backbone upon helix formation. These results indicate the polarizable force field to more accurately model peptide-folding cooperativity based on its physically realistic treatment of electronic polarizability.
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Affiliation(s)
- Jing Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland.
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38
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Joachimiak LA, Walzthoeni T, Liu CW, Aebersold R, Frydman J. The structural basis of substrate recognition by the eukaryotic chaperonin TRiC/CCT. Cell 2015; 159:1042-1055. [PMID: 25416944 DOI: 10.1016/j.cell.2014.10.042] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 08/17/2014] [Accepted: 10/20/2014] [Indexed: 12/20/2022]
Abstract
The eukaryotic chaperonin TRiC (also called CCT) is the obligate chaperone for many essential proteins. TRiC is hetero-oligomeric, comprising two stacked rings of eight different subunits each. Subunit diversification from simpler archaeal chaperonins appears linked to proteome expansion. Here, we integrate structural, biophysical, and modeling approaches to identify the hitherto unknown substrate-binding site in TRiC and uncover the basis of substrate recognition. NMR and modeling provided a structural model of a chaperonin-substrate complex. Mutagenesis and crosslinking-mass spectrometry validated the identified substrate-binding interface and demonstrate that TRiC contacts full-length substrates combinatorially in a subunit-specific manner. The binding site of each subunit has a distinct, evolutionarily conserved pattern of polar and hydrophobic residues specifying recognition of discrete substrate motifs. The combinatorial recognition of polypeptides broadens the specificity of TRiC and may direct the topology of bound polypeptides along a productive folding trajectory, contributing to TRiC's unique ability to fold obligate substrates.
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Affiliation(s)
- Lukasz A Joachimiak
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA.
| | - Thomas Walzthoeni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland; Ph.D. Program in Molecular Life Sciences, University of Zurich/ETH Zurich, 8057 Zurich, Switzerland
| | - Corey W Liu
- Stanford Magnetic Resonance Laboratory, Stanford University, Stanford, CA 94305, USA
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
| | - Judith Frydman
- Department of Biology and Genetics, Stanford University, Stanford, CA 94305, USA.
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39
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Verma RK, Prabh ND, Sankararamakrishnan R. Intra-helical salt-bridge and helix destabilizing residues within the same helical turn: Role of functionally important loop E half-helix in channel regulation of major intrinsic proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1436-49. [PMID: 25797519 DOI: 10.1016/j.bbamem.2015.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 03/08/2015] [Accepted: 03/13/2015] [Indexed: 12/26/2022]
Abstract
The superfamily of major intrinsic proteins (MIPs) includes aquaporin (AQP) and aquaglyceroporin (AQGP) and it is involved in the transport of water and neutral solutes across the membrane. Diverse MIP sequences adopt a unique hour-glass fold with six transmembrane helices (TM1 to TM6) and two half-helices (LB and LE). Loop E contains one of the two conserved NPA motifs and contributes two residues to the aromatic/arginine selectivity filter. Function and regulation of majority of MIP channels are not yet characterized. We have analyzed the loop E region of 1468 MIP sequences and their structural models from six different organism groups. They can be phylogenetically clustered into AQGPs, AQPs, plant MIPs and other MIPs. The LE half-helix in all AQGPs contains an intra-helical salt-bridge and helix-breaking residues Gly/Pro within the same helical turn. All non-AQGPs lack this salt-bridge but have the helix destabilizing Gly and/or Pro in the same positions. However, the segment connecting LE half-helix and TM6 is longer by 10-15 residues in AQGPs compared to all non-AQGPs. We speculate that this longer loop in AQGPs and the LE half-helix of non-AQGPs will be relatively more flexible and this could be functionally important. Molecular dynamics simulations on glycerol-specific GlpF, water-transporting AQP1, its mutant and a fungal AQP channel confirm these predictions. Thus two distinct regions of loop E, one in AQGPs and the other in non-AQGPs, seem to be capable of modulating the transport. These regions can also act in conjunction with other extracellular residues/segments to regulate MIP channel transport.
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Affiliation(s)
- Ravi Kumar Verma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Neel Duti Prabh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Ramasubbu Sankararamakrishnan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India; Centre of Excellence for Chemical Biology, Indian Institute of Technology Kanpur, Kanpur 208016, India.
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40
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Zhou CY, Jiang F, Wu YD. Residue-Specific Force Field Based on Protein Coil Library. RSFF2: Modification of AMBER ff99SB. J Phys Chem B 2014; 119:1035-47. [DOI: 10.1021/jp5064676] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chen-Yang Zhou
- College
of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Yun-Dong Wu
- College
of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
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41
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Molecular dynamics simulation study of solvation effects of water and trifluoroethanol on gamma-aminobutyric acid (GABA). J Mol Liq 2014. [DOI: 10.1016/j.molliq.2014.04.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Hazel A, Chipot C, Gumbart JC. Thermodynamics of Deca-alanine Folding in Water. J Chem Theory Comput 2014; 10:2836-2844. [PMID: 25061447 PMCID: PMC4095909 DOI: 10.1021/ct5002076] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Indexed: 11/28/2022]
Abstract
![]()
The determination of the folding
dynamics of polypeptides and proteins
is critical in characterizing their functions in biological systems.
Numerous computational models and methods have been developed for
studying structure formation at the atomic level. Due to its small
size and simple structure, deca-alanine is used as a model system
in molecular dynamics (MD) simulations. The free energy of unfolding
in vacuum has been studied extensively using the end-to-end distance
of the peptide as the reaction coordinate. However, few studies have
been conducted in the presence of explicit solvent. Previous results
show a significant decrease in the free energy of extended conformations
in water, but the α-helical state is still notably favored over
the extended state. Although sufficient in vacuum, we show that end-to-end
distance is incapable of capturing the full complexity of deca-alanine
folding in water. Using α-helical content as a second reaction
coordinate, we deduce a more descriptive free-energy landscape, one
which reveals a second energy minimum in the extended conformations
that is of comparable free energy to the α-helical state. Equilibrium
simulations demonstrate the relative stability of the extended and
α-helical states in water as well as the transition between
the two states. This work reveals both the necessity and challenge
of determining a proper reaction coordinate to fully characterize
a given process.
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Affiliation(s)
- Anthony Hazel
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Christophe Chipot
- Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States ; Laboratoire Associé International Centre National de la Recherche Scientifique - Unité Mixte de Recherche , N°7565, BP 70239, 54506 Vandœuvre-lès-Nancy, France
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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43
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Effects of side chains in helix nucleation differ from helix propagation. Proc Natl Acad Sci U S A 2014; 111:6636-41. [PMID: 24753597 DOI: 10.1073/pnas.1322833111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Helix-coil transition theory connects observable properties of the α-helix to an ensemble of microstates and provides a foundation for analyzing secondary structure formation in proteins. Classical models account for cooperative helix formation in terms of an energetically demanding nucleation event (described by the σ constant) followed by a more facile propagation reaction, with corresponding s constants that are sequence dependent. Extensive studies of folding and unfolding in model peptides have led to the determination of the propagation constants for amino acids. However, the role of individual side chains in helix nucleation has not been separately accessible, so the σ constant is treated as independent of sequence. We describe here a synthetic model that allows the assessment of the role of individual amino acids in helix nucleation. Studies with this model lead to the surprising conclusion that widely accepted scales of helical propensity are not predictive of helix nucleation. Residues known to be helix stabilizers or breakers in propagation have only a tenuous relationship to residues that favor or disfavor helix nucleation.
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44
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de la Torre C, Agostini A, Mondragón L, Orzáez M, Sancenón F, Martínez-Máñez R, Marcos MD, Amorós P, Pérez-Payá E. Temperature-controlled release by changes in the secondary structure of peptides anchored onto mesoporous silica supports. Chem Commun (Camb) 2014; 50:3184-6. [DOI: 10.1039/c3cc49421g] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Changes in the conformation of a peptide anchored onto the external surface of MCM-41 nanoparticles are used to design temperature-controlled delivery systems.
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Affiliation(s)
- Cristina de la Torre
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Unidad Mixta Universidad Politécnica de Valencia-Universidad de Valencia
- Spain
- Departamento de Química
- Universidad Politécnica de Valencia
| | - Alessandro Agostini
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Unidad Mixta Universidad Politécnica de Valencia-Universidad de Valencia
- Spain
- Departamento de Química
- Universidad Politécnica de Valencia
| | - Laura Mondragón
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Unidad Mixta Universidad Politécnica de Valencia-Universidad de Valencia
- Spain
- Departamento de Química
- Universidad Politécnica de Valencia
| | - Mar Orzáez
- Centro de Investigación Principe Felipe
- Laboratorio de Péptidos y Proteinas. Avda. Autopista del Saler 16
- 46012 Valencia, Spain
- Instituto de Biomedicina de Valencia
- IBV-CSIC
| | - Félix Sancenón
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Unidad Mixta Universidad Politécnica de Valencia-Universidad de Valencia
- Spain
- Departamento de Química
- Universidad Politécnica de Valencia
| | - Ramón Martínez-Máñez
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Unidad Mixta Universidad Politécnica de Valencia-Universidad de Valencia
- Spain
- Departamento de Química
- Universidad Politécnica de Valencia
| | - María D. Marcos
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM)
- Unidad Mixta Universidad Politécnica de Valencia-Universidad de Valencia
- Spain
- Departamento de Química
- Universidad Politécnica de Valencia
| | - Pedro Amorós
- Institut de Ciència dels Materials (ICMUV)
- Universitat de València
- 46071 Valencia, Spain
| | - Enríque Pérez-Payá
- Centro de Investigación Principe Felipe
- Laboratorio de Péptidos y Proteinas. Avda. Autopista del Saler 16
- 46012 Valencia, Spain
- Instituto de Biomedicina de Valencia
- IBV-CSIC
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Modi V, Sankararamakrishnan R. Antiapoptotic Bcl-2 homolog CED-9 in Caenorhabditis elegans
: Dynamics of BH3 and CED-4 binding regions and comparison with mammalian antiapoptotic Bcl-2 proteins. Proteins 2013; 82:1035-47. [DOI: 10.1002/prot.24476] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 10/16/2013] [Accepted: 11/04/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Vivek Modi
- Department of Biological Sciences & Bioengineering; Indian Institute of Technology Kanpur; Kanpur 208016 India
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Ioannou F, Leontidis E, Archontis G. Helix Formation by Alanine-Based Peptides in Pure Water and Electrolyte Solutions: Insights from Molecular Dynamics Simulations. J Phys Chem B 2013; 117:9866-76. [DOI: 10.1021/jp406231g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Filippos Ioannou
- Department
of Chemistry, and ‡Deparment of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
| | - Epameinondas Leontidis
- Department
of Chemistry, and ‡Deparment of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
| | - Georgios Archontis
- Department
of Chemistry, and ‡Deparment of Physics, University of Cyprus, PO20537, CY1678, Nicosia, Cyprus
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47
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Sun T, Wei C, Neo NWC, Zhang D. Misfolding of a polyalanine variant due to lack of electrostatic polarization effects. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1354-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Penas C, Pazos E, Mascareñas JL, Vázquez ME. A Folding-Based Approach for the Luminescent Detection of a Short RNA Hairpin. J Am Chem Soc 2013; 135:3812-4. [DOI: 10.1021/ja400270a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Cristina Penas
- Centro Singular
de Investigación en Química
Biolóxica e Materiais Moleculares (CIQUS), Departamento de
Química Orgánica and Unidad Asociada al CSIC, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Elena Pazos
- Centro Singular
de Investigación en Química
Biolóxica e Materiais Moleculares (CIQUS), Departamento de
Química Orgánica and Unidad Asociada al CSIC, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - José L. Mascareñas
- Centro Singular
de Investigación en Química
Biolóxica e Materiais Moleculares (CIQUS), Departamento de
Química Orgánica and Unidad Asociada al CSIC, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - M. Eugenio Vázquez
- Centro Singular
de Investigación en Química
Biolóxica e Materiais Moleculares (CIQUS), Departamento de
Química Orgánica and Unidad Asociada al CSIC, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
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Spagnuolo MS, Di Stasi R, De Rosa L, Maresca B, Cigliano L, D'Andrea LD. Analysis of the haptoglobin binding region on the apolipoprotein A-I-derived P2a peptide. J Pept Sci 2013; 19:220-6. [PMID: 23420675 DOI: 10.1002/psc.2487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/08/2013] [Accepted: 01/10/2013] [Indexed: 11/10/2022]
Abstract
Apolipoprotein A-I (ApoA-I) is the main protein component of the high density lipoproteins and it plays an important role in the reverse cholesterol transport. In particular, it stimulates cholesterol efflux from peripheral cells toward liver and activates the enzyme lecithin-cholesterol acyltransferase (LCAT). Haptoglobin (Hpt), a plasma α2-glycoprotein belonging to the family of acute-phase proteins, binds to ApoA-I inhibiting the stimulation of the enzyme LCAT. Previously, we reported that a synthetic peptide, P2a, binds to and displaces Hpt from ApoA-I restoring the LCAT cholesterol esterification activity in the presence of Hpt. Here, we investigate the molecular determinants underlining the interaction between Hpt and P2a peptide. Analysis of truncated P2a analogs showed that P2a sequence can only be slight reduced in length at the N-terminal to preserve the ability of binding to Hpt. Binding assays showed that charged residues are not involved in Hpt recognition; actually, E146A and D157A substitutions increase the binding affinity to Hpt. Biological characterization of the corresponding P2a peptide analogs, Apo146 and Apo157, showed that the two peptides interfere with Hpt binding to HDL and are more effective than P2a peptide in rescue LCAT activity from Hpt inhibition. This result suggests novel hints to design peptides with anti-atherogenic activity.
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Michalek M, Salnikov ES, Werten S, Bechinger B. Membrane interactions of the amphipathic amino terminus of huntingtin. Biochemistry 2013; 52:847-58. [PMID: 23305455 DOI: 10.1021/bi301325q] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The amino-terminal domain of huntingtin (Htt17), located immediately upstream of the decisive polyglutamine tract, strongly influences important properties of this large protein and thereby the development of Huntington's disease. Htt17 markedly increases polyglutamine aggregation rates and the level of huntingtin's interactions with biological membranes. Htt17 adopts a largely helical conformation in the presence of membranes, and this structural transition was used to quantitatively analyze membrane association as a function of lipid composition. The apparent membrane partitioning constants increased in the presence of anionic lipids but decreased with increasing amounts of cholesterol. When membrane permeabilization was tested, a pronounced dye release was observed from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) vesicles and 75:25 (molar ratio) POPC/1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine vesicles but not across bilayers that better mimic cellular membranes. Solid-state nuclear magnetic resonance structural investigations indicated that the Htt17 α-helix adopts an alignment parallel to the membrane surface, and that the tilt angle (∼75°) was nearly constant in all of the membranes that were investigated. Furthermore, the addition of Htt17 resulted in a decrease in the lipid order parameter in all of the membranes that were investigated. The lipid interactions of Htt17 have pivotal implications for membrane anchoring and functional properties of huntingtin and concomitantly the development of the disease.
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Affiliation(s)
- Matthias Michalek
- Membrane Biophysics and NMR Chemistry Institute UMR7177, University of Strasbourg/CNRS International Center for Frontier Research in Chemistry, 1 rue Blaise Pascal, Strasbourg, France
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