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Comparison of design strategies for α-helix backbone modification in a protein tertiary fold.

Tavenor NA, Reinert ZE, Lengyel GA, Griffith BD, Horne WS
Chem Commun (Camb) 52 3789-92 (2016)
Related entries: 5hfy, 5hg2

Cited: 20 times
EuropePMC logo PMID: 26853882

Abstract

We report here the comparison of five classes of unnatural amino acid building blocks for their ability to be accommodated into an α-helix in a protein tertiary fold context. High-resolution structural characterization and analysis of folding thermodynamics yield new insights into the relationship between backbone composition and folding energetics in α-helix mimetics and suggest refined design rules for engineering the backbones of natural sequences.

Articles - 5hi1 mentioned but not cited (4)

  1. Foldamer Tertiary Structure through Sequence-Guided Protein Backbone Alteration. George KL, Horne WS. Acc Chem Res 51 1220-1228 (2018)
  2. Comparison of design strategies for α-helix backbone modification in a protein tertiary fold. Tavenor NA, Reinert ZE, Lengyel GA, Griffith BD, Horne WS. Chem Commun (Camb) 52 3789-3792 (2016)
  3. Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα. Lee S, Devamani T, Song HD, Sandhu M, Larsen A, Sommese R, Jain A, Vaidehi N, Sivaramakrishnan S. J Biol Chem 292 16300-16309 (2017)
  4. A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics. Bogetti AT, Piston HE, Leung JMG, Cabalteja CC, Yang DT, DeGrave AJ, Debiec KT, Cerutti DS, Case DA, Horne WS, Chong LT. J Chem Phys 153 064101 (2020)


Reviews citing this publication (3)

  1. Systematic Targeting of Protein-Protein Interactions. Modell AE, Blosser SL, Arora PS. Trends Pharmacol Sci 37 702-713 (2016)
  2. Analysis of folded structure and folding thermodynamics in heterogeneous-backbone proteomimetics. Santhouse JR, Rao SR, Horne WS. Methods Enzymol 656 93-122 (2021)
  3. Amino acid modifications for conformationally constraining naturally occurring and engineered peptide backbones: Insights from the Protein Data Bank. Di Costanzo L, Dutta S, Burley SK. Biopolymers 109 e23230 (2018)

Articles citing this publication (13)

  1. The effects of thioamide backbone substitution on protein stability: a study in α-helical, β-sheet, and polyproline II helical contexts. Walters CR, Szantai-Kis DM, Zhang Y, Reinert ZE, Horne WS, Chenoweth DM, Petersson EJ. Chem Sci 8 2868-2877 (2017)
  2. Heterogeneous-Backbone Foldamer Mimics of Zinc Finger Tertiary Structure. George KL, Horne WS. J Am Chem Soc 139 7931-7938 (2017)
  3. Designing cooperatively folded abiotic uni- and multimolecular helix bundles. De S, Chi B, Granier T, Qi T, Maurizot V, Huc I. Nat Chem 10 51-57 (2018)
  4. Receptor selectivity from minimal backbone modification of a polypeptide agonist. Liu S, Cheloha RW, Watanabe T, Gardella TJ, Gellman SH. Proc Natl Acad Sci U S A 115 12383-12388 (2018)
  5. Thermodynamic Scale of β-Amino Acid Residue Propensities for an α-Helix-like Conformation. Fisher BF, Hong SH, Gellman SH. J Am Chem Soc 140 9396-9399 (2018)
  6. Heterogeneous-Backbone Foldamer Mimics of a Computationally Designed, Disulfide-Rich Miniprotein. Cabalteja CC, Mihalko DS, Horne WS. Chembiochem 20 103-110 (2019)
  7. Vagabond: bond-based parametrization reduces overfitting for refinement of proteins. Ginn HM. Acta Crystallogr D Struct Biol 77 424-437 (2021)
  8. Incorporation of α-methylated amino acids into Apolipoprotein A-I mimetic peptides improves their helicity and cholesterol efflux potential. Islam R, Sviridov DO, Drake SK, Tunyi J, Abdoulaeva G, Freeman LA, Pastor RW, Remaley AT. Biochem Biophys Res Commun 526 349-354 (2020)
  9. Implications of the unfolded state in the folding energetics of heterogeneous-backbone protein mimetics. Santhouse JR, Leung JMG, Chong LT, Horne WS. Chem Sci 13 11798-11806 (2022)
  10. Chemical Shifts of Artificial Monomers Used to Construct Heterogeneous-Backbone Protein Mimetics in Random Coil and Folded States. Rao SR, Harmon TW, Heath SL, Wolfe JA, Santhouse JR, O'Brien GL, Distefano AN, Reinert ZE, Horne WS. Pept Sci (Hoboken) 115 e24297 (2023)
  11. Development of CHARMM Additive Potential Energy Parameters for α-Methyl Amino Acids. Pane AJ, Yu W, Aytenfisu A, Tunyi J, Venable RM, MacKerell AD, Pastor RW. J Phys Chem B 125 11687-11696 (2021)
  12. Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein. Santhouse JR, Leung JMG, Chong LT, Horne WS. Chem Sci 15 675-682 (2024)
  13. Heterogeneous-Backbone Proteomimetic Analogues of Lasiocepsin, a Disulfide-Rich Antimicrobial Peptide with a Compact Tertiary Fold. Cabalteja CC, Lin Q, Harmon TW, Rao SR, Di YP, Horne WS. ACS Chem Biol 17 987-997 (2022)


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