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Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines.

Islam MM, Sohya S, Noguchi K, Yohda M, Kuroda Y
Proc Natl Acad Sci U S A 105 15334-9 (2008)
Cited: 16 times
EuropePMC logo PMID: 18829434

Abstract

We report the high-resolution crystal structures of an extensively simplified variant of bovine pancreatic trypsin inhibitor containing 20 alanines (BPTI-20st) and a reference single-disulfide-bonded variant (BPTI-[5,55]st) at, respectively, 1.39 and 1.09 A resolutions. The sequence was simplified based on the results of an alanine scanning experiment, as reported previously. The effects of the multiple alanine substitutions on the overall backbone structure were surprisingly small (C(alpha) atom RMSD of 0.53 A) being limited to small local structural perturbations. Both BPTI variants retained a wild-type level of trypsin inhibitory activity. The side-chain configurations of residues buried in the hydrophobic cores (<30% accessible surface area) were almost perfectly retained in both BPTI-20st and BPTI-[5,55]st, indicating that neither multiple alanine replacements nor the removal of the disulfide bonds affected their precise placements. However, the side chains of three partially buried residues (Q31, R20, and to some extent Y21) and several unburied residues rearranged into alternative dense-packing structures, suggesting some plasticity in their shape complementarity. These results indicate that a protein sequence simplified over its entire length can retain its densely packed, native side-chain structure, and suggest that both the design and fold recognition of natively folded proteins may be easier than previously thought.

Reviews - 2zjx mentioned but not cited (1)

  1. Recent Advances in Studying Toll-like Receptors with the Use of Computational Methods. Bzówka M, Bagrowska W, Góra A. J Chem Inf Model 63 3669-3687 (2023)

Articles - 2zjx mentioned but not cited (4)

  1. A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex. Dalton KM, Crosson S. Biochemistry 49 2205-2215 (2010)
  2. Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines. Islam MM, Sohya S, Noguchi K, Yohda M, Kuroda Y. Proc Natl Acad Sci U S A 105 15334-15339 (2008)
  3. Hydrophobic surface residues can stabilize a protein through improved water-protein interactions. Islam MM, Kobayashi K, Kidokoro SI, Kuroda Y. FEBS J 286 4122-4134 (2019)
  4. Thermodynamic and structural analysis of highly stabilized BPTIs by single and double mutations. Islam MM, Sohya S, Noguchi K, Kidokoro S, Yohda M, Kuroda Y. Proteins 77 962-970 (2009)


Articles citing this publication (11)

  1. Funneling and frustration in the energy landscapes of some designed and simplified proteins. Truong HH, Kim BL, Schafer NP, Wolynes PG. J Chem Phys 139 121908 (2013)
  2. Metal-binding loop length and not sequence dictates structure. Sato K, Li C, Salard I, Thompson AJ, Banfield MJ, Dennison C. Proc Natl Acad Sci U S A 106 5616-5621 (2009)
  3. High resolution crystal structure of dengue-3 envelope protein domain III suggests possible molecular mechanisms for serospecific antibody recognition. Elahi M, Islam MM, Noguchi K, Yohda M, Kuroda Y. Proteins 81 1090-1095 (2013)
  4. Computational prediction and experimental characterization of a "size switch type repacking" during the evolution of dengue envelope protein domain III (ED3). Elahi M, Islam MM, Noguchi K, Yohda M, Toh H, Kuroda Y. Biochim Biophys Acta 1844 585-592 (2014)
  5. Letter Amorphous protein aggregation monitored using fluorescence self-quenching. Jozawa H, Kabir MG, Zako T, Maeda M, Chiba K, Kuroda Y. FEBS Lett 590 3501-3509 (2016)
  6. A systematic mutational analysis identifies a 5-residue proline tag that enhances the in vivo immunogenicity of a non-immunogenic model protein. Rahman N, Islam MM, Kibria MG, Unzai S, Kuroda Y. FEBS Open Bio 10 1947-1956 (2020)
  7. Biochemical and biophysical characterization of an unexpected bacteriolytic activity of VanX, a member of the vancomycin-resistance vanA gene cluster. Sohya S, Kamioka T, Fujita C, Maki T, Ohta Y, Kuroda Y. J Biol Chem 289 35686-35694 (2014)
  8. Crystal structures of highly simplified BPTIs provide insights into hydration-driven increase of unfolding enthalpy. Islam MM, Yohda M, Kidokoro SI, Kuroda Y. Sci Rep 7 41205 (2017)
  9. Does stoichiometry drive protein folding? Ventura S. J Biomol Struct Dyn 28 655-6; discussion 669-674 (2011)
  10. Improved protein splicing reaction for low solubility protein fragments without insertion of native extein residues. Kamioka T, Tawa M, Sohya S, Yamazaki T, Kuroda Y. Biopolymers 92 465-470 (2009)
  11. Free-Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics. Kulkarni M, Söderhjelm P. J Chem Theory Comput 19 6605-6618 (2023)


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