123l › Citations

Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme.

Blaber M, Lindstrom JD, Gassner N, Xu J, Heinz DW, Matthews BW
Biochemistry 32 11363-73 (1993)
Related entries: 118l, 119l, 120l, 122l, 125l, 126l, 127l, 128l, 206l, 221l, 224l

Cited: 59 times
EuropePMC logo PMID: 8218201

Abstract

In order to determine the thermodynamic cost of introducing a polar group within the core of a protein, a series of nine Ala-->Ser and 3 Val-->Thr substitutions was constructed in T4 lysozyme. The sites were all within alpha-helices but ranged from fully solvent-exposed to totally buried. The range of destabilization incurred by the Ala-->Ser substitutions was found to be very similar to that for the Val-->Thr replacements. For the solvent-exposed and partly exposed sites the destabilization was modest (approximately less than 0.5 kcal/mol). For the completely buried sites the destabilization was larger, but variable (approximately 1-3 kcal/mol). Crystal structure determinations showed that the Ala-->Ser mutant structures were, in general, very similar to their wild-type counterparts, even though the replacements introduce a hydroxyl group. This is in part because the introduced serines are all within alpha-helices and at congested sites can avoid steric clashes with surrounding atoms by making a hydrogen bond to a backbone carbonyl oxygen in the preceding turn of the helix. The three substituted threonine side chains essentially superimpose on their valine counterparts but display somewhat larger conformational adjustments. The results illustrate how a protein structure will adapt in different ways to avoid the presence of an unsatisfied hydrogen bond donor or acceptor. In the most extreme case, Val 149-->Thr, which is also the most destabilizing variant (delta delta G = 2.8 kcal/mol), a water molecule is incorporated in the mutant structure in order to provide a hydrogen-bonding partner. The results are consistent with the view that many hydrogen bonds within proteins contribute only marginally to stability but that noncharged polar groups that lack a hydrogen-bonding partner are very destabilizing (delta delta G approximately greater than 3 kcal/mol). Supportive of other studies, the alpha-helix propensity of alanine is seen to be higher than that of serine (delta delta G = 0.46 +/- 0.04 kcal/mol), while threonine and valine are similar in alpha-helix propensity.

Articles - 123l mentioned but not cited (4)

  1. Genome of invertebrate iridescent virus type 3 (mosquito iridescent virus). Delhon G, Tulman ER, Afonso CL, Lu Z, Becnel JJ, Moser BA, Kutish GF, Rock DL. J Virol 80 8439-8449 (2006)
  2. Genomic and proteomic analysis of invertebrate iridovirus type 9. Wong CK, Young VL, Kleffmann T, Ward VK. J Virol 85 7900-7911 (2011)
  3. The hemoglobins of the trematodes Fasciola hepatica and Paramphistomum epiclitum: a molecular biological, physico-chemical, kinetic, and vaccination study. Dewilde S, Ioanitescu AI, Kiger L, Gilany K, Marden MC, Van Doorslaer S, Vercruysse J, Pesce A, Nardini M, Bolognesi M, Moens L. Protein Sci 17 1653-1662 (2008)
  4. Genome Characteristics of Two Ranavirus Isolates from Mandarin Fish and Largemouth Bass. Yu XD, Ke F, Zhang QY, Gui JF. Pathogens 12 730 (2023)


Reviews citing this publication (4)

  1. Energetics of protein folding. Baldwin RL. J Mol Biol 371 283-301 (2007)
  2. Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges. Guedes IA, Pereira FSS, Dardenne LE. Front Pharmacol 9 1089 (2018)
  3. Core-packing constraints, hydrophobicity and protein design. Baldwin EP, Matthews BW. Curr Opin Biotechnol 5 396-402 (1994)
  4. Engineering surface loops of proteins--a preferred strategy for obtaining new enzyme function. el Hawrani AS, Moreton KM, Sessions RB, Clarke AR, Holbrook JJ. Trends Biotechnol 12 207-211 (1994)

Articles citing this publication (51)

  1. Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove. Fremont DH, Stura EA, Matsumura M, Peterson PA, Wilson IA. Proc Natl Acad Sci U S A 92 2479-2483 (1995)
  2. Hydrogen bonding stabilizes globular proteins. Myers JK, Pace CN. Biophys J 71 2033-2039 (1996)
  3. Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity. Pokala N, Handel TM. J Mol Biol 347 203-227 (2005)
  4. Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2. López-Hernández E, Serrano L. Fold Des 1 43-55 (1996)
  5. Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins. Gao J, Bosco DA, Powers ET, Kelly JW. Nat Struct Mol Biol 16 684-690 (2009)
  6. Energetics of hydrogen bonding in proteins: a model compound study. Habermann SM, Murphy KP. Protein Sci 5 1229-1239 (1996)
  7. Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior. Loladze VV, Ermolenko DN, Makhatadze GI. J Mol Biol 320 343-357 (2002)
  8. Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme. Zhang XJ, Matthews BW. Protein Sci 3 1031-1039 (1994)
  9. The molecular basis of thrombin allostery revealed by a 1.8 A structure of the "slow" form. Huntington JA, Esmon CT. Structure 11 469-479 (2003)
  10. Statistical and molecular dynamics studies of buried waters in globular proteins. Park S, Saven JG. Proteins 60 450-463 (2005)
  11. Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D, Petsko GA, Herschlag D. PLoS Biol 4 e99 (2006)
  12. Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme. Vetter IR, Baase WA, Heinz DW, Xiong JP, Snow S, Matthews BW. Protein Sci 5 2399-2415 (1996)
  13. Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation. Pokala N, Handel TM. Protein Sci 13 925-936 (2004)
  14. Exploring steric constraints on protein mutations using MAGE/PROBE. Word JM, Bateman RC, Presley BK, Lovell SC, Richardson DC. Protein Sci 9 2251-2259 (2000)
  15. Design of highly stable functional GroEL minichaperones. Wang Q, Buckle AM, Foster NW, Johnson CM, Fersht AR. Protein Sci 8 2186-2193 (1999)
  16. Coupling protein stability and protein function in Escherichia coli CspA. Hillier BJ, Rodriguez HM, Gregoret LM. Fold Des 3 87-93 (1998)
  17. The introduction of strain and its effects on the structure and stability of T4 lysozyme. Liu R, Baase WA, Matthews BW. J Mol Biol 295 127-145 (2000)
  18. Are the parameters of various stabilization factors estimated from mutant human lysozymes compatible with other proteins? Funahashi J, Takano K, Yutani K. Protein Eng 14 127-134 (2001)
  19. Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme. Xu J, Baase WA, Quillin ML, Baldwin EP, Matthews BW. Protein Sci 10 1067-1078 (2001)
  20. Solvation energetics and conformational change in EF-hand proteins. Ababou A, Desjarlais JR. Protein Sci 10 301-312 (2001)
  21. Structural coupling between FKBP12 and buried water. Szep S, Park S, Boder ET, Van Duyne GD, Saven JG. Proteins 74 603-611 (2009)
  22. Thermodynamics of trimer-of-hairpins formation by the SIV gp41 envelope protein. Jelesarov I, Lu M. J Mol Biol 307 637-656 (2001)
  23. Dynamics of lysozyme structure network: probing the process of unfolding. Ghosh A, Brinda KV, Vishveshwara S. Biophys J 92 2523-2535 (2007)
  24. Bioinformatic analysis of α/β-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities. Suplatov DA, Besenmatter W, Svedas VK, Svendsen A. Protein Eng Des Sel 25 689-697 (2012)
  25. Absolute hydration free energies of blocked amino acids: implications for protein solvation and stability. König G, Bruckner S, Boresch S. Biophys J 104 453-462 (2013)
  26. Interatomic potentials and solvation parameters from protein engineering data for buried residues. Lomize AL, Reibarkh MY, Pogozheva ID. Protein Sci 11 1984-2000 (2002)
  27. Role of a solvent-exposed aromatic cluster in the folding of Escherichia coli CspA. Rodriguez HM, Vu DM, Gregoret LM. Protein Sci 9 1993-2000 (2000)
  28. Thermodynamic analysis of the effect of selective monodeamidation at asparagine 67 in ribonuclease A. Catanzano F, Graziano G, Capasso S, Barone G. Protein Sci 6 1682-1693 (1997)
  29. Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor. Barratt E, Bronowska A, Vondrásek J, Cerný J, Bingham R, Phillips S, Homans SW. J Mol Biol 362 994-1003 (2006)
  30. Structural and energetic consequences of mutations in a solvated hydrophobic cavity. Adamek DH, Guerrero L, Blaber M, Caspar DL. J Mol Biol 346 307-318 (2005)
  31. A double-deletion method to quantifying incremental binding energies in proteins from experiment: example of a destabilizing hydrogen bonding pair. Campos LA, Cuesta-López S, López-Llano J, Falo F, Sancho J. Biophys J 88 1311-1321 (2005)
  32. Approaching protein design with multisite λ dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme. Hayes RL, Vilseck JZ, Brooks CL. Protein Sci 27 1910-1922 (2018)
  33. Engineering a more thermostable blue light photo receptor Bacillus subtilis YtvA LOV domain by a computer aided rational design method. Song X, Wang Y, Shu Z, Hong J, Li T, Yao L. PLoS Comput Biol 9 e1003129 (2013)
  34. Alanine-scanning mutagenesis of the beta-sheet region of phage T4 lysozyme suggests that tertiary context has a dominant effect on beta-sheet formation. He MM, Wood ZA, Baase WA, Xiao H, Matthews BW. Protein Sci 13 2716-2724 (2004)
  35. Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme. Mooers BH, Baase WA, Wray JW, Matthews BW. Protein Sci 18 871-880 (2009)
  36. A single aromatic core mutation converts a designed "primitive" protein from halophile to mesophile folding. Longo LM, Tenorio CA, Kumru OS, Middaugh CR, Blaber M. Protein Sci 24 27-37 (2015)
  37. Pathogenic mutations in the carboxyl-terminal domain of glutaryl-CoA dehydrogenase: effects on catalytic activity and the stability of the tetramer. Westover JB, Goodman SI, Frerman FE. Mol Genet Metab 79 245-256 (2003)
  38. Rational and computational design of stabilized variants of cyanovirin-N that retain affinity and specificity for glycan ligands. Patsalo V, Raleigh DP, Green DF. Biochemistry 50 10698-10712 (2011)
  39. High polar content of long buried blocks of sequence in protein domains suggests selection against amyloidogenic non-polar sequences. Patki AU, Hausrath AC, Cordes MH. J Mol Biol 362 800-809 (2006)
  40. The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog. Cuneo MJ, Tian Y, Allert M, Hellinga HW. BMC Struct Biol 8 20 (2008)
  41. Mispacking and the Fitness Landscape of the Green Fluorescent Protein Chromophore Milieu. Banerjee S, Schenkelberg CD, Jordan TB, Reimertz JM, Crone EE, Crone DE, Bystroff C. Biochemistry 56 736-747 (2017)
  42. Structural consequences of site-directed mutagenesis in flexible protein domains: NMR characterization of the L(55,56)S mutant of RhoGDI. Golovanov AP, Hawkins D, Barsukov I, Badii R, Bokoch GM, Lian LY, Roberts GC. Eur J Biochem 268 2253-2260 (2001)
  43. Comment Can proteins be turned inside-out? Matthews BW. Nat Struct Biol 2 85-86 (1995)
  44. Tolerance to the substitution of buried apolar residues by charged residues in the homologous protein structures. Balaji S, Aruna S, Srinivasan N. Proteins 53 783-791 (2003)
  45. Using affinity chromatography to engineer and characterize pH-dependent protein switches. Sagermann M, Chapleau RR, DeLorimier E, Lei M. Protein Sci 18 217-228 (2009)
  46. Structural consequences of an amino acid deletion in the B1 domain of protein G. O'Neil KT, Bach AC, DeGrado WF. Proteins 41 323-333 (2000)
  47. Modulating the DNA affinity of Elk-1 with computationally selected mutations. Park S, Boder ET, Saven JG. J Mol Biol 348 75-83 (2005)
  48. T4 lysozyme-facilitated crystallization of the human molybdenum cofactor-dependent enzyme mARC. Kubitza C, Ginsel C, Bittner F, Havemeyer A, Clement B, Scheidig AJ. Acta Crystallogr F Struct Biol Commun 74 337-344 (2018)
  49. "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics. Bazzoli A, Karanicolas J. J Comput Chem 38 1321-1331 (2017)
  50. Analysis of the dynamics of rhizomucor miehei lipase at different temperatures. Peters GH, Toxvaerd S, Andersen KV, Svendsen A. J Biomol Struct Dyn 16 1003-1018 (1999)
  51. Identification and characterization of two classes of G1 β-bulge. Leader DP, Milner-White EJ. Acta Crystallogr D Struct Biol 77 217-223 (2021)


Related citations provided by authors (2)

  1. Control of Enzyme Activity by an Engineered Disulfide Bond. Matsumura M, Matthews BW Science 243 792- (1989)
  2. Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution. Weaver LH, Matthews BW J. Mol. Biol. 193 189- (1987)

Quick links