Empirical relationships between protein structure and carboxyl pK<sub>a</sub> values in proteins

Forsyth, William R.; Antosiewicz, Jan; Robertson, Andrew D.

doi:10.1002/prot.10174

Cited by 199 publications

(248 citation statements)

References 121 publications

Supporting

Mentioning

231

Contrasting

Order By: Relevance

“…It is at least a formal possibility that the carboxylate side chain of Glu-3 is actually protonated when the wild-type enzyme binds oxoG and that the acidic -OH group of the protonated carboxyl hydrogen bonds to O 8 of oxoG in a manner much like the amide -NH 2 of Gln-3. An attraction of this scenario is that it would obviously facilitate the glycosyl transfer step by activating the oxoG leaving group; a difficulty is that carboxylates involved in helix-capping interactions have unusually high acidity and are therefore unlikely to be protonated (32).…”

Section: Resultsmentioning

confidence: 99%

DNA Lesion Recognition by the Bacterial Repair Enzyme MutM

Fromme

Verdine

2003

Journal of Biological Chemistry

171

327

View full text Add to dashboard Cite

MutM is a bacterial DNA glycosylase that removes the mutagenic lesion 8-oxoguanine (oxoG) from duplex DNA. The means of oxoG recognition by MutM (also known as Fpg) is of fundamental interest, in light of the vast excess of normal guanine bases present in genomic DNA. The crystal structure of a recognition-competent but catalytically inactive version of MutM in complex with oxoG-containing DNA reveals the structural basis for recognition. MutM binds the oxoG nucleoside in the syn glycosidic configuration and distinguishes oxoG from guanine by reading out the protonation state of the N7 atom. The segment of MutM principally responsible for oxoG recognition is a flexible loop, suggesting that conformational mobility influences lesion recognition and catalysis. Furthermore, the structure of MutM in complex with DNA containing an alternative substrate, dihydrouracil, demonstrates how MutM is able to recognize lesions other than oxoG.The reactive byproducts of aerobic respiration oxidize DNA to generate a number of deleterious adducts, among which the most widely studied is 8-oxoguanine (oxoG). 1 Because oxoG mispairs with adenine during replication, this oxidative lesion is a source of G⅐C to T⅐A transversion mutations. Nearly all organisms possess enzymes that safeguard against the genotoxic effects of oxoG. The oxoG resistance pathway in bacteria, known as the "GO" system, comprises three components: MutT, MutY, and MutM (1-4). MutT hydrolyzes oxo-dGTP to oxodGMP and inorganic pyrophosphate so as to prevent de novo incorporation of oxoG into the genome during DNA replication. MutY initiates the repair of misreplicated oxoG⅐A pairs in DNA by catalyzing hydrolytic excision of the adenine base. MutM (also known as Fpg) is a bifunctional DNA glycosylase/lyase that catalyzes complete excision of oxoG lesion nucleosides when paired opposite C in DNA via a complex multistep reaction cascade. Most eukaryotes possess a GO system related to that in bacteria, with orthologous versions of MutT and MutY; however, in higher organisms, MutM is replaced by the functionally analogous but structurally unrelated enzyme Ogg1 (5, 6). Orthologs of MutM have been discovered in mammals, but these do not appear to be primarily involved in oxoG repair (7-10).Recent structural studies of MutM-DNA complexes have revealed the overall architecture of the protein-DNA complex. These structures have also provided insights into the general features of lesion presentation to the MutM active site, suggesting that the oxoG nucleoside is swiveled out of the DNA helix during repair, a theme common throughout the structural biology of base excision DNA repair. A segment of the protein near the active site is disordered in the DNA-bound MutM structures lacking an oxoG nucleobase, yet is ordered in the absence of DNA, thus leading to the tantalizing suggestion that induced fit might contribute to lesion base recognition. Understanding the structural determinants of lesion recognition by MutM has been hampered by the fact that none of the available high re...

show abstract

Section: Resultsmentioning

confidence: 99%

DNA Lesion Recognition by the Bacterial Repair Enzyme MutM

Fromme

Verdine

2003

Journal of Biological Chemistry

171

327

View full text Add to dashboard Cite

show abstract

“…[3][4][5][6][7][8][9][10] Most of the pK values for folded proteins have been measured directly using techniques based on nuclear magnetic resonance (NMR). [11][12][13] A smaller number have been measured using indirect techniques. 14,15 In several recent papers, summaries of these results have been given: 212 carboxyl groups 13 ; 314 values.…”

Section: Introductionmentioning

confidence: 99%

A summary of the measured pK values of the ionizable groups in folded proteins

2008

View full text Add to dashboard Cite

We tabulated 541 measured pK values reported in the literature for the Asp, Glu, His, Cys, Tyr, and Lys side chains, and the C and N termini of 78 folded proteins. The majority of these values are for the Asp, Glu, and His side chains. The average pK values are Asp 3.5 6 1.2 (139); Glu 4.2 6 0.9 (153); His 6.6 6 1.0 (131); Cys 6.8 6 2.7 (25); Tyr 10.3 6 1.2 (20); Lys 10.5 6 1.1 (35); Cterminus 3.3 6 0.8 (22) and N-terminus 7.7 6 0.5 (16). We compare these results with the measured pK values of these groups in alanine pentapeptides, and comment on our overall findings.

show abstract

“…Interestingly, an amino acid residue located at different positions in a folded protein often exhibits different degrees of acidity or basicity. For example, an acidic residue, such as cysteine or aspartic acid, located at or near the N-terminus of a helix is often more acidic than that at or near the C-terminus [5,[7][8][9][10][11]. A wealth of studies on the acid-base properties of helical peptides have been carried out in condensed phase, in particular in aqueous solutions [11][12][13].…”

mentioning

confidence: 99%

Gas-phase acidities of cysteine-polyglycine peptides: The effect of the cysteine position

Morishetti

Huang

Yates

et al. 2010

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

The sequence and conformational effects on the gas-phase acidities of peptides have been studied by using two pairs of isomeric cysteine-polyglycine peptides, CysGly 3,4 NH 2 and Gly 3,4 CysNH 2 . The extended Cooks kinetic method was employed to determine the gas-phase acidities using a triple quadrupole mass spectrometer with an electrospray ionization source. The ion activation was achieved via collision-induced dissociation experiments. The deprotonation enthalpies (⌬ acid H) were determined to be 323.9 Ϯ 2.5 kcal/mol (CysGly 3 NH 2 ), 319.2 Ϯ 2.3 kcal/mol (CysGly 4 NH 2 ), 333.8 Ϯ 2.1 kcal/mol (Gly 3 CysNH 2 ), and 321.9 Ϯ 2.8 kcal/mol (Gly 4 CysNH 2 ), respectively. The corresponding deprotonation entropies (⌬ acid S) of the peptides were estimated. The gas-phase acidities (⌬ acid G) were derived to be 318.4 Ϯ 2.5 kcal/mol (CysGly 3 NH 2 ), 314.9 Ϯ 2.3 kcal/mol (CysGly 4 NH 2 ), 327.5 Ϯ 2.1 kcal/mol (Gly 3 CysNH 2 ), and 317.4 Ϯ 2.8 kcal/mol (Gly 4 CysNH 2 ), respectively. Conformations and energetic information of the neutral and anionic peptides were calculated through simulated annealing (Tripos), geometry optimization (AM1), and single point energy calculations (B3LYP/6-31ϩG(d)), respectively. Both neutral and deprotonated peptides adopt many possible conformations of similar energies. All neutral peptides are mainly random coils. The two C-cysteine anionic peptides, Gly 3,4 (Cys-H) Ϫ NH 2 , are also random coils. The two N-cysteine anionic peptides, (Cys-H) Ϫ Gly 3,4 NH 2 , may exist in both random coils and stretched helices. The two N-cysteine peptides, CysGly 3 NH 2 and CysGly 4 NH 2 , are significantly more acidic than the corresponding C-terminal cysteine ones, Gly 3 CysNH 2 and Gly 4 CysNH 2 . The stronger acidities of the former may come from the greater stability of the thiolate anion resulting from the interaction with the helix-macrodipole, in addition to the hydrogen bonding interactions. (J Am Soc Mass Spectrom 2010, 21, 603-614)

show abstract

Empirical relationships between protein structure and carboxyl pK_a values in proteins

Cited by 199 publications

References 121 publications

DNA Lesion Recognition by the Bacterial Repair Enzyme MutM

DNA Lesion Recognition by the Bacterial Repair Enzyme MutM

A summary of the measured pK values of the ionizable groups in folded proteins

Gas-phase acidities of cysteine-polyglycine peptides: The effect of the cysteine position

Contact Info

Product

Resources

About

Empirical relationships between protein structure and carboxyl pKa values in proteins

Cited by 199 publications

References 121 publications

DNA Lesion Recognition by the Bacterial Repair Enzyme MutM

DNA Lesion Recognition by the Bacterial Repair Enzyme MutM

A summary of the measured pK values of the ionizable groups in folded proteins

Gas-phase acidities of cysteine-polyglycine peptides: The effect of the cysteine position

Contact Info

Product

Resources

About

Empirical relationships between protein structure and carboxyl pK_a values in proteins