1
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Sun JW, Thomas JS, Monkovic JM, Gibson H, Nagapurkar A, Frezzo JA, Katyal P, Punia K, Mahoudinobar F, Renfrew PD, Montclare JK. Supercharged coiled-coil protein with N-terminal decahistidine tag boosts siRNA complexation and delivery efficiency of a lipoproteoplex. J Pept Sci 2024:e3594. [PMID: 38499991 DOI: 10.1002/psc.3594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
Short interfering RNA (siRNA) therapeutics have soared in popularity due to their highly selective and potent targeting of faulty genes, providing a non-palliative approach to address diseases. Despite their potential, effective transfection of siRNA into cells requires the assistance of an accompanying vector. Vectors constructed from non-viral materials, while offering safer and non-cytotoxic profiles, often grapple with lackluster loading and delivery efficiencies, necessitating substantial milligram quantities of expensive siRNA to confer the desired downstream effects. We detail the recombinant synthesis of a diverse series of coiled-coil supercharged protein (CSP) biomaterials systematically designed to investigate the impact of two arginine point mutations (Q39R and N61R) and decahistidine tags on liposomal siRNA delivery. The most efficacious variant, N8, exhibits a twofold increase in its affinity to siRNA and achieves a twofold enhancement in transfection activity with minimal cytotoxicity in vitro. Subsequent analysis unveils the destabilizing effect of the Q39R and N61R supercharging mutations and the incorporation of C-terminal decahistidine tags on α-helical secondary structure. Cross-correlational regression analyses reveal that the amount of helical character in these mutants is key in N8's enhanced siRNA complexation and downstream delivery efficiency.
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Affiliation(s)
- Jonathan W Sun
- Department of Chemistry, New York University, New York, New York, USA
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Joseph S Thomas
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Julia M Monkovic
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Halle Gibson
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Akash Nagapurkar
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Joseph A Frezzo
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Priya Katyal
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Kamia Punia
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
| | - Farbod Mahoudinobar
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Jin Kim Montclare
- Department of Chemistry, New York University, New York, New York, USA
- Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, Brooklyn, New York, USA
- Department of Radiology, NYU Grossman School of Medicine, New York, New York, USA
- Department of Biomaterials, NYU College of Dentistry, New York, New York, USA
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2
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Nag A, Mafi A, Das S, Yu MB, Alvarez-Villalonga B, Kim SK, Su Y, Goddard WA, Heath JR. Stereochemical engineering yields a multifunctional peptide macrocycle inhibitor of Akt2 by fine-tuning macrocycle-cell membrane interactions. Commun Chem 2023; 6:95. [PMID: 37202473 DOI: 10.1038/s42004-023-00890-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 04/26/2023] [Indexed: 05/20/2023] Open
Abstract
Macrocycle peptides are promising constructs for imaging and inhibiting extracellular, and cell membrane proteins, but their use for targeting intracellular proteins is typically limited by poor cell penetration. We report the development of a cell-penetrant high-affinity peptide ligand targeted to the phosphorylated Ser474 epitope of the (active) Akt2 kinase. This peptide can function as an allosteric inhibitor, an immunoprecipitation reagent, and a live cell immunohistochemical staining reagent. Two cell penetrant stereoisomers were prepared and shown to exhibit similar target binding affinities and hydrophobic character but 2-3-fold different rates of cell penetration. Experimental and computational studies resolved that the ligands' difference in cell penetration could be assigned to their differential interactions with cholesterol in the membrane. These results expand the tool kit for designing new chiral-based cell-penetrant ligands.
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Affiliation(s)
- Arundhati Nag
- California Institute of Technology, Pasadena, CA, USA
- Clark University, Worcester, MA, USA
| | - Amirhossein Mafi
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, USA
| | - Samir Das
- California Institute of Technology, Pasadena, CA, USA
- Clark University, Worcester, MA, USA
| | - Mary Beth Yu
- California Institute of Technology, Pasadena, CA, USA
| | | | - Soo-Kyung Kim
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, USA
| | - Yapeng Su
- California Institute of Technology, Pasadena, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - William A Goddard
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, USA
| | - James R Heath
- California Institute of Technology, Pasadena, CA, USA.
- Institute for Systems Biology, Seattle, WA, USA.
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3
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Zhuang Y, Bureau HR, Lopez C, Bucher R, Quirk S, Hernandez R. Energetics and structure of alanine-rich α-helices via adaptive steered molecular dynamics. Biophys J 2021; 120:2009-2018. [PMID: 33775636 PMCID: PMC8204395 DOI: 10.1016/j.bpj.2021.03.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/03/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022] Open
Abstract
The energetics and hydrogen bonding profiles of the helix-to-coil transition were found to be an additive property and to increase linearly with chain length, respectively, in alanine-rich α-helical peptides. A model system of polyalanine repeats was used to establish this hypothesis for the energetic trends and hydrogen bonding profiles. Numerical measurements of a synthesized polypeptide Ac-Y(AEAAKA)kF-NH2 and a natural α-helical peptide a2N (1-17) provide evidence of the hypothesis's generality. Adaptive steered molecular dynamics was employed to investigate the mechanical unfolding of all of these alanine-rich polypeptides. We found that the helix-to-coil transition is primarily dependent on the breaking of the intramolecular backbone hydrogen bonds and independent of specific side-chain interactions and chain length. The mechanical unfolding of the α-helical peptides results in a turnover mechanism in which a 310-helical structure forms during the unfolding, remaining at a near constant population and thereby maintaining additivity in the free energy. The intermediate partially unfolded structures exhibited polyproline II helical structure as previously seen by others. In summary, we found that the average force required to pull alanine-rich α-helical peptides in between the endpoints-namely the native structure and free coil-is nearly independent of the length or the specific primary structure.
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Affiliation(s)
- Yi Zhuang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland
| | - Hailey R Bureau
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland
| | - Christine Lopez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland
| | - Ryan Bucher
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland
| | | | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland; Departments of Chemical and Biomolecular Engineering, and Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland.
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4
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Ardejani MS, Powers ET, Kelly JW. Using Cooperatively Folded Peptides To Measure Interaction Energies and Conformational Propensities. Acc Chem Res 2017; 50:1875-1882. [PMID: 28723063 DOI: 10.1021/acs.accounts.7b00195] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The rates and equilibria of the folding of biopolymers are determined by the conformational preferences of the subunits that make up the sequence of the biopolymer and by the interactions that are formed in the folded state in aqueous solution. Because of the centrality of these processes to life, quantifying conformational propensities and interaction strengths is vitally important to understanding biology. In this Account, we describe our use of peptide model systems that fold cooperatively yet are small enough to be chemically synthesized to measure such quantities. The necessary measurements are made by perturbing an interaction or conformation of interest by mutation and measuring the difference between the folding free energies of the wild type (in which the interaction or conformation is undisturbed) and the mutant model peptides (in which the interaction has been eliminated or the conformational propensities modified). With the proper controls and provided that the peptide model system in question folds via a two-state process, these folding free energy differences can be accurate measures of interaction strengths or conformational propensities. This method has the advantage of having high sensitivity and high dynamic range because the energies of interest are coupled to folding free energies, which can be measured with precisions on the order of a few tenths of a kilocalorie by well-established biophysical methods, like chaotrope or thermal denaturation studies monitored by fluorescence or circular dichroism. In addition, because the model peptides can be chemically synthesized, the full arsenal of natural and unnatural amino acids can be used to tune perturbations to be as drastic or subtle as desired. This feature is particularly noteworthy because it enables the use of analytical tools developed for physical organic chemistry, especially linear free energy relationships, to decompose interaction energies into their component parts to obtain a deeper understanding of the forces that drive interactions in biopolymers. We have used this approach, primarily with the WW domain derived from the human Pin1 protein as our model system, to assess hydrogen bond strengths (especially those formed by backbone amides), the dependence of hydrogen bond strengths on the environment in which they form, β-turn propensities of both natural sequences and small molecule β-turn mimics, and the energetics of carbohydrate-protein interactions. In each case, the combination of synthetic accessibility, the ease of measuring folding energies, and the robustness of the structure of the Pin1 WW domain to mutation enabled us to obtain incisive measurements of quantities that have been challenging to measure by other methods.
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Affiliation(s)
- Maziar S. Ardejani
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Evan T. Powers
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffery W. Kelly
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- The
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La
Jolla, California 92037, United States
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5
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Ireta J. Polyalanine α-helix microsolvation: assessing the energy of the peptide desolvation penalty with density functional theory. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1981-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Pohl G, Asensio A, Dannenberg JJ. Capping parallel β-sheets of acetyl(Ala)6NH2 with an acetyl(Ala)5ProNH2 can arrest the growth of the sheet, suggesting a potential for curtailing amyloid growth. An ONIOM and density functional theory study. Biochemistry 2014; 53:617-23. [PMID: 24422496 PMCID: PMC3985835 DOI: 10.1021/bi401366w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present ONIOM calculations using B3LYP/d95(d,p) as the high level and AM1 as the medium level on parallel β-sheets containing four strands of Ac-AAAAAA-NH2 capped with either Ac-AAPAAA-NH2 or Ac-AAAPAA-NH2. Because Pro can form H-bonds from only one side of the peptide linkage (that containing the C═O H-bond acceptor), only one of the two Pro-containing strands can favorably add to the sheet on each side. Surprisingly, when the sheet is capped with AAPAAA-NH2 at one edge, the interaction between the cap and sheet is slightly more stabilizing than that of another all Ala strand. Breaking down the interaction enthalpies into H-bonding and distortion energies shows the favorable interaction to be due to lower distortion energies in both the strand and the four-stranded sheet. Because another strand would be inhibited for attachment to the other side of the capping (Pro-containing) strand, we suggest the possible use of Pro residues in peptides designed to arrest the growth of many amyloids.
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Affiliation(s)
- Gabor Pohl
- Department of Chemistry, City University of New York, Hunter College and the Graduate School , 695 Park Avenue, New York, New York 10065, United States
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7
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Ignacio-de Leon PA, Cichelli JA, Abelow AE, Zharov I. Pore-Filled Nanoporous Silica Colloidal Films with Enantioselective Permeability. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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8
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Shigeno M, Kushida Y, Yamaguchi M. Molecular Thermal Hysteresis in Helix-Dimer Formation of Sulfonamidohelicene Oligomers in Solution. Chemistry 2013; 19:10226-34. [DOI: 10.1002/chem.201204556] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 04/22/2013] [Indexed: 11/08/2022]
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9
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Rossi M, Scheffler M, Blum V. Impact of Vibrational Entropy on the Stability of Unsolvated Peptide Helices with Increasing Length. J Phys Chem B 2013; 117:5574-84. [DOI: 10.1021/jp402087e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Matthias Scheffler
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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10
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Olivares-Quiroz L. Thermodynamics of ideal proteinogenic homopolymer chains as a function of the energy spectrum E, helical propensity ω and enthalpic energy barrier. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:155103. [PMID: 23515207 DOI: 10.1088/0953-8984/25/15/155103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A reformulation and generalization of the Zwanzig model (ZW model) for ideal homopolymer chains poly-X, where X represents any of the twenty naturally occurring proteinogenic amino acid residues is presented. This reformulation and generalization provides a direct connection between coarse-grained parameters originally proposed in the ZW model with variables from the Lifson-Roig (LR) theory, such as the helical propensity per residue ω, and new variables introduced here, such as the energy gap Δ between unfolded and folded structures, as well as the ratio f of the energy scales involved. This enables us to discover the relevance of the energy spectrum E to the onset of configurational phase transitions. From the configurational partition function Q, thermodynamic properties such as the configurational entropy S, specific heat v and average energy <E> are calculated in terms of the number of residues K, temperature T, helical propensity ω and energy barrier ΔH for different poly-X chains in vacuo. Results obtained here provide substantial evidence that configurational phase transitions for ideal poly-X chains correspond to first-order phase transitions. An anomalous behavior of the thermodynamic functions <E>, Cv, S with respect to the number K of residues is also highlighted. On-going methods of solution are outlined.
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Affiliation(s)
- L Olivares-Quiroz
- Universidad Autónoma de la Ciudad de México, Campus Cuautepec, Av La Corona 320, Col Loma Alta CP 07160 DF, Mexico.
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11
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Marianski M, Asensio A, Dannenberg JJ. Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives. J Chem Phys 2012; 137:044109. [PMID: 22852599 DOI: 10.1063/1.4737517] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O...N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95∗∗ to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).
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Affiliation(s)
- Mateusz Marianski
- Department of Chemistry, City University of New York - Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, USA
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12
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Opioid glycopeptide analgesics derived from endogenous enkephalins and endorphins. Future Med Chem 2012; 4:205-26. [PMID: 22300099 DOI: 10.4155/fmc.11.195] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Over the past two decades, potent and selective analgesics have been developed from endogenous opioid peptides. Glycosylation provides an important means of modulating interaction with biological membranes, which greatly affects the pharmacodynamics and pharmacokinetics of the resulting glycopeptide analogues. Furthermore, manipulation of the membrane affinity allows penetration of cellular barriers that block efficient drug distribution, including the blood-brain barrier. Extremely potent and selective opiate agonists have been developed from endogenous peptides, some of which show great promise as drug candidates.
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13
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Pandey PR, Roy S. Distinctions in early stage unwinding mechanisms of zwitterionic, capped, and neutral forms of different α-helical homopolymeric peptides. J Phys Chem B 2012; 116:4731-40. [PMID: 22448707 DOI: 10.1021/jp301556x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations of α-helical polyalanine, polyleucine, polylysine, and poly(glutamic acid) with different forms of terminal groups in water at 300 K showed sharp distinctions in their unwinding mechanisms. Zwitterionic, capped, and neutral forms of polyalanine, polyleucine, and polylysine have been explored to elucidate their unwinding mechanism at very early stage, e.g., initial time window. Role of water in the unwinding mechanisms of the various helices has been envisaged. Also, it is evident from our calculations that the short- and long-range nonbonded interactions among the side chains is an important factor determining the unwinding mechanisms of the various homopolymeric α-helices. These findings can be helpful in constructing predictive models for understanding of the unwinding of α-helical proteins and peptides.
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Affiliation(s)
- Prithvi Raj Pandey
- Physical Chemistry Division, National Chemical Laboratory , Pune 411008, India
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14
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Marianski M, Dannenberg JJ. Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory. J Phys Chem B 2012; 116:1437-45. [PMID: 22201227 DOI: 10.1021/jp209177u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water molecules that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models.
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Affiliation(s)
- Mateusz Marianski
- Department of Chemistry, City University of New York-Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, USA
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15
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López GE, Colón-Díaz I, Cruz A, Ghosh S, Nicholls SB, Viswanathan U, Hardy JA, Auerbach SM. Modeling Nonaqueous Proton Wires Built from Helical Peptides: Biased Proton Transfer Driven by Helical Dipoles. J Phys Chem A 2012; 116:1283-8. [DOI: 10.1021/jp210208m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gustavo E. López
- Department of Chemistry, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico 00681
- Department of Chemistry, Lehman College-CUNY, Bronx, New York 10034, United States
| | - Inara Colón-Díaz
- Department of Chemistry, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico 00681
| | - Anthony Cruz
- Department of Chemistry, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico 00681
- Department of Chemistry, Lehman College-CUNY, Bronx, New York 10034, United States
| | - Sumana Ghosh
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Samantha B. Nicholls
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Usha Viswanathan
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Jeanne A. Hardy
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Scott M. Auerbach
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
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16
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Bernacki JP, Murphy RM. Length-dependent aggregation of uninterrupted polyalanine peptides. Biochemistry 2011; 50:9200-11. [PMID: 21932820 DOI: 10.1021/bi201155g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyalanine (polyA) is the third-most prevalent homopeptide repeat in eukaryotes, behind polyglutamine and polyasparagine. Abnormal expansion of the polyA repeat is linked to at least nine human diseases, and the disease mechanism likely involves enhanced length-dependent aggregation. Because of the simplicity of its side chain, polyA has been a favorite target of computational studies, and because of their tendency to fold into α-helix, peptides containing polyA-rich domains have been a popular experimental subject. However, experimental studies on uninterrupted polyA are very limited. We synthesized polyA peptides containing uninterrupted sequences of 7 to 25 alanines (A7 to A25) and characterized their length-dependent conformation and aggregation properties. The peptides were primarily disordered, with a modest component of α-helix that increased with increasing length. From measurements of mean distance spanned by the polyA segment, we concluded that physiological buffers are neutral solvents for shorter polyA peptides and poor solvents for longer peptides. At moderate concentration and near-physiological temperature, polyA assembled into soluble oligomers, with a sharp transition in oligomer physical properties between A19 and A25. With A19, oligomers were large, contained only a small fraction of the total peptide mass, and slowly grew into loose clusters, while A25 rapidly and completely assembled into small stable oligomers of ~7 nm radius. At high temperatures, A19 assembled into fibrils, but A25 precipitated as dense, micrometer-sized particles. A comparison of these results to those obtained with polyglutamine peptides of similar design sheds light on the role of the side chain in regulating conformation and aggregation.
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Affiliation(s)
- Joseph P Bernacki
- Department of Chemical and Biological Engineering, University of Wisconsin, Madison, Wisconsin 53706, United States
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17
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Chen YF, Dannenberg JJ. The effect of polarization on multiple hydrogen-bond formation in models of self-assembling materials. J Comput Chem 2011; 32:2890-5. [PMID: 21717481 DOI: 10.1002/jcc.21870] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/01/2011] [Accepted: 05/23/2011] [Indexed: 01/27/2023]
Abstract
We report density functional theory calculations at the B3LYP/D95(d,p) level on several different cyclic H-bonding dimers, where the monomers of each are connected by a pair of N-H···O=C H-bonding interactions, and the H-bonding donors and acceptors on each monomer are separated by polarizable spacers. Depending on the structures, the individual H-bonds vary in strength (enthalpy) by over a factor of four, from 2.41 to 10.99 kcal/mol. We attribute most of the variation in interaction energies to differences in the extent of polarization due to each of the H-bonds, which can either combine constructively or destructively. The dipole-dipole interactions between the pair of H-bonds also contribute somewhat to the relative stabilities. The relevance of these results to the design of self-assembling materials is discussed.
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Affiliation(s)
- Yung-Fou Chen
- Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10065, USA
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18
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Tkatchenko A, Rossi M, Blum V, Ireta J, Scheffler M. Unraveling the stability of polypeptide helices: critical role of van der Waals interactions. PHYSICAL REVIEW LETTERS 2011; 106:118102. [PMID: 21469900 DOI: 10.1103/physrevlett.106.118102] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Indexed: 05/30/2023]
Abstract
Folding and unfolding processes are important for the functional capability of polypeptides and proteins. In contrast with a physiological environment (solvated or condensed phases), an in vacuo study provides well-defined "clean room" conditions to analyze the intramolecular interactions that largely control the structure, stability, and folding or unfolding dynamics. Here we show that a proper consideration of van der Waals (vdW) dispersion forces in density-functional theory (DFT) is essential, and a recently developed DFT+vdW approach enables long time-scale ab initio molecular dynamics simulations at an accuracy close to "gold standard" quantum-chemical calculations. The results show that the inclusion of vdW interactions qualitatively changes the conformational landscape of alanine polypeptides, and greatly enhances the thermal stability of helical structures, in agreement with gas-phase experiments.
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Affiliation(s)
- Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
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19
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Cheng RP, Girinath P, Suzuki Y, Kuo HT, Hsu HC, Wang WR, Yang PA, Gullickson D, Wu CH, Koyack MJ, Chiu HP, Weng YJ, Hart P, Kokona B, Fairman R, Lin TE, Barrett O. Positional Effects on Helical Ala-Based Peptides. Biochemistry 2010; 49:9372-84. [DOI: 10.1021/bi101156j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard P. Cheng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Prashant Girinath
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Yuta Suzuki
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Hsiou-Ting Kuo
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Hao-Chun Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Ren Wang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Po-An Yang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Donald Gullickson
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Cheng-Hsun Wu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Marc J. Koyack
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Hsien-Po Chiu
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
| | - Yi-Jen Weng
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Pier Hart
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania 19041
| | - Tzu-En Lin
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Olivia Barrett
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000
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20
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Balamurugan K, Gopalakrishnan R, Raman SS, Subramanian V. Exploring the Changes in the Structure of α-Helical Peptides Adsorbed onto a Single Walled Carbon Nanotube Using Classical Molecular Dynamics Simulation. J Phys Chem B 2010; 114:14048-58. [DOI: 10.1021/jp106177n] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- K. Balamurugan
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai- 600020, India
| | - R. Gopalakrishnan
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai- 600020, India
| | - S. Sundar Raman
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai- 600020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai- 600020, India
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21
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Nasr KA, Schubert CR, Török M, Kennedy RJ, Kemp DS. Helix-coil energetics for helix formers and breakers reflect context and temperature: mutants of helically robust, guest-sensitive homopeptide hosts. Biopolymers 2010; 91:311-20. [PMID: 19117030 DOI: 10.1002/bip.21129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The natural amino acids are primarily helix breakers at the low assignment temperatures characteristic of many studies, but recent genomic analyses of thermophilic proteins suggest that at high temperatures, some breakers may become strong helix formers. Moreover, the breaker/former inventory has not been previously characterized at the physiologically relevant temperature of 37 degrees C. The versatility of 13C==O NMR chemical shifts as helicity reporters allows construction of two mutant peptide series, tailored to expand the range of temperature assignments for helical propensities and derived from the core hosts tL-Ala9XxxAla9-tL and tL-AlaNva4XxxNva4Ala9-tL, Nva=norvaline. For three limiting guests Xxx, the helix former Nva and the breakers Gly and Pro, we report wXxx[T] assignments at seven temperatures from 2 to 80 degrees C, validating our reasoning and paving the way for assignment of a definitive wXxx[T] data-base.
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Affiliation(s)
- Khaled A Nasr
- Department of Chemistry, Room 6-433, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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22
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Plumley JA, Dannenberg JJ. The Importance of Hydrogen Bonding between the Glutamine Side Chains to the Formation of Amyloid VQIVYK Parallel β-Sheets: An ONIOM DFT/AM1 Study. J Am Chem Soc 2010; 132:1758-9. [DOI: 10.1021/ja909690a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua A. Plumley
- Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10065
| | - J. J. Dannenberg
- Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10065
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23
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Kulp J, Clark T. Engineering a β-Helical d,l-Peptide for Folding in Polar Media. Chemistry 2009; 15:11867-77. [DOI: 10.1002/chem.200901129] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Moreau RJ, Schubert CR, Nasr KA, Török M, Miller JS, Kennedy RJ, Kemp DS. Context-independent, temperature-dependent helical propensities for amino acid residues. J Am Chem Soc 2009; 131:13107-16. [PMID: 19702302 PMCID: PMC2770013 DOI: 10.1021/ja904271k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Assigned from data sets measured in water at 2, 25, and 60 degrees C containing (13)C=O NMR chemical shifts and [theta](222) ellipticities, helical propensities are reported for the 20 genetically coded amino acids, as well as for norvaline and norleucine. These have been introduced by chemical synthesis at central sites within length-optimized, spaced, solubilized Ala(19) hosts. The resulting polyalanine-derived, quantitative propensity sets express for each residue its temperature-dependent but context-independent tendency to forego a coil state and join a preexisting helical conformation. At 2 degrees C their rank ordering is: P << G < H < C, T, N < S < Y, F, W < V, D < K < Q < I < R, M < L < E < A; at 60 degrees C the rank becomes: H, P < G < C < R, K < T, Y, F < N, V < S < Q < W, D < I, M < E < A < L. The DeltaDeltaG values, kcal/mol, relative to alanine, for the cluster T, N, S, Y, F, W, V, D, Q, imply that at 2 degrees C all are strong breakers: DeltaDeltaG(mean) = +0.63 +/- 0.11, but at 60 degrees C their breaking tendencies are dramatically attenuated and converge toward the mean: DeltaDeltaG(mean) = +0.25 +/- 0.07. Accurate modeling of helix-rich proteins found in thermophiles, mesophiles, and organisms that flourish near 0 degrees C thus requires appropriately matched propensity sets. Comparisons are offered between the temperature-dependent propensity assignments of this study and those previously assigned by the Scheraga group; the special problems that attend propensity assignments for charged residues are illustrated by lysine guest data; and comparisons of errors in helicity assignments from shifts and ellipticity data show that the former provide superior precision and accuracy.
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Affiliation(s)
- Robert J Moreau
- Department of Chemistry, Room 6-433, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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25
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Ireta J, Scheffler M. Density functional theory study of the conformational space of an infinitely long polypeptide chain. J Chem Phys 2009; 131:085104. [DOI: 10.1063/1.3207815] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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26
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Goto H, Furusho Y, Miwa K, Yashima E. Double helix formation of oligoresorcinols in water: thermodynamic and kinetic aspects. J Am Chem Soc 2009; 131:4710-9. [PMID: 19334774 DOI: 10.1021/ja808585y] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We previously reported that the oligoresorcinols formed double-stranded helices in neutral water through interstrand aromatic interactions. In the present study, we synthesized a new series of oligomers from the 2mer to the 15mer to explore the thermodynamics, kinetics, and mechanism of the double helix formation of the oligoresorcinols in water. The double helix formation was dependent on the chain length of the oligomers and significantly affected by solvent, pH, salt, and temperature. The free energy change (-DeltaG) for the double helix formation linearly increased with the chain length from the 4mer to the 11mer (DeltaDeltaG = -0.94 kcal mol(-1) unit(-1)), whereas it did not change for the oligomers longer than the 11mer. The van't Hoff analysis of the 9mer revealed that the double helix formation was an enthalpically driven process (DeltaH = -27 +/- 1.5 kcal mol(-1) and DeltaS = -70 +/- 5 cal mol(-1) K(-1)), which was consistent with the upfield shifts in the (1)H NMR spectra and the hypochromicity of the absorption spectra as a result of the interstrand aromatic interactions in water. Furthermore, the kinetic analysis of the chain exchange reaction between the double helices of the optically active and optically inactive 11mers revealed a small DeltaS(double dagger), suggesting that the chain exchange proceeds not via the dissociation-association pathway, but via the direct exchange pathway.
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Affiliation(s)
- Hidetoshi Goto
- Yashima Super-structured Helix Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Nagoya 464-8603, Japan
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27
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Tsai MIH, Xu Y, Dannenberg JJ. Ramachandran revisited. DFT energy surfaces of diastereomeric trialanine peptides in the gas phase and aqueous solution. J Phys Chem B 2009; 113:309-18. [PMID: 19072621 DOI: 10.1021/jp8063646] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report DFT calculations at the B3LYP/D95(d,p) level on the gas phase, aqueous solvation and solvated energies as functions of the central psi and phi dihedral angles (in steps of 5 degrees each) of acetyl-(L)Ala-(L)Ala-(L)Ala-NH(2) (3AL) and its diastereomer, acetyl-(L)Ala-(D)Ala-(L)Ala-NH(2) (3AD). In addition to structures without internal H-bonds (C(5) interactions are neglected), many (95) structures containing internal H-bonds were completely optimized. The only minima for non-H-bonding structures in the gas phase correspond to extended beta-strands for both diastereomers. Some (but not all) structures with internal H-bonds are more stable than those without them. The energy landscapes for the solvated species show multiple minima for the non-H-bonding species and a single minimum for the H-bonding species (3(10)-helix), suggesting that the equilibrium conformational mixture in water be composed of the extended beta-strand, polyproline II, 3(10)-helix, and alpha-helix-like (with no H-bonds) conformations which are all within about 1 kcal/mol of each other. Most H-bonding structures are destabilized relative to the non-H-bonding structures in aqueous solution, but some with large dipole moments are not. The large dipole moment of the alpha-helix-like conformation leads to its increased stability in water (vs the gas phase). Significant qualitative and quantitative differences are reported for the energy landscapes of the two diastereomers when one is compared with the mirror image of the other landscape (particularly in the beta-turn region), suggesting that the differences in the energies of the unfolded peptides need to be considered when considering the stabilities of folded peptides and proteins with single amino acid mutations.
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Affiliation(s)
- Midas I-Hsien Tsai
- Department of Chemistry, City University of New York, New York 10065, USA
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28
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A 310-helix single turn enforced by crosslinking of lysines with 1,1′-ferrocenedicarboxylic acid. J Organomet Chem 2009. [DOI: 10.1016/j.jorganchem.2008.11.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Zhong J, Chau Y. Antitumor activity of a membrane lytic peptide cyclized with a linker sensitive to membrane type 1-matrix metalloproteinase. Mol Cancer Ther 2008; 7:2933-40. [DOI: 10.1158/1535-7163.mct-08-0528] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Song K, Stewart JM, Fesinmeyer RM, Andersen NH, Simmerling C. Structural insights for designed alanine-rich helices: comparing NMR helicity measures and conformational ensembles from molecular dynamics simulation. Biopolymers 2008; 89:747-60. [PMID: 18428207 DOI: 10.1002/bip.21004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The temperature dependence of helical propensities for the peptides Ac-ZGG-(KAAAA)(3)X-NH(2) (Z = Y or G, X = A, K, and D-Arg) were studied both experimentally and by MD simulations. Good agreement is observed in both the absolute helical propensities as well as relative helical content along the sequence; the global minimum on the calculated free energy landscape corresponds to a single alpha-helical conformation running from K4 to A18 with some terminal fraying, particularly at the C-terminus. Energy component analysis shows that the single helix state has favorable intramolecular electrostatic energy due to hydrogen bonds, and that less-favorable two-helix globular states have favorable solvation energy. The central lysine residues do not appear to increase helicity; however, both experimental and simulation studies show increasing helicity in the series X = Ala --> Lys --> D-Arg. This C-capping preference was also experimentally confirmed in Ac-(KAAAA)(3)X-GY-NH(2) and (KAAAA)(3)X-GY-NH(2) sequences. The roles of the C-capping groups, and of lysines throughout the sequence, in the MD-derived ensembles are analyzed in detail.
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Affiliation(s)
- Kun Song
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
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31
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Stewart JM, Lin JC, Andersen NH. Lysine and arginine residues do not increase the helicity of alanine-rich peptide helices. Chem Commun (Camb) 2008:4765-7. [PMID: 18830486 DOI: 10.1039/b807101b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The helix-disfavoring, versus alanine, propagation values of lysine (0.8) and arginine (1.0) residues placed centrally in an (Ala)(9) unit have been measured by (13)C NMR.
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Affiliation(s)
- James M Stewart
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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32
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Raman SS, Vijayaraj R, Parthasarathi R, Subramanian V. Helix forming tendency of valine substituted poly-alanine: a molecular dynamics investigation. J Phys Chem B 2008; 112:9100-4. [PMID: 18597521 DOI: 10.1021/jp7119813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this study, classical molecular dynamics simulations have been carried out on the valine (guest) substituted poly alanine (host) using the host-guest peptide approach to understand the role of valine in the formation and stabilization of helix. Valine has been substituted in the host peptide starting from N terminal to C terminal. Various structural parameters have been obtained from the molecular dynamics simulation to understand the tolerance of helical motif to valine. Depending on the position of valine in the host peptide, it stabilizes (or destabilizes) the formation of the helical structure. The substitution of valine in the poly alanine at some positions has no effect on the helix formation (deformation). It is interesting to observe the coexistence of 3 10 and alpha-helix in the peptides due to the dynamical nature of the hydrogen bonding interaction and sterical interactions.
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Affiliation(s)
- S Sundar Raman
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020 India
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33
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Toward the Design of Highly Efficient, Readily Accessible Peptide N-caps for the Induction of Helical Conformations. Int J Pept Res Ther 2007. [DOI: 10.1007/s10989-006-9073-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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