TY - JOUR
T1 - Short carboxylic acid-carboxylate hydrogen bonds can have fully localized protons
AU - Lin, Jiusheng
AU - Pozharski, Edwin
AU - Wilson, Mark A.
N1 - Funding Information:
Figure 4. E. coli YajL has a COOH−−OOC H-bond with an ambiguous protonation state. Panels A and B show the two independent Glu14−Asp23 H-bonds in the ASU. 2mFo − DFc electron density at 0.98 Å resolution contoured at 1.0σ (blue) and 5.3σ (purple) and mFo − DFc electron density contoured at 2.5σ (green). Primes indicate residues contributed by the other protomer, whose carbon atoms are colored gray. The modeled hydrogen atom on Glu14 is colored white in each panel and agrees closely with the location of an mFo − DFc electron density peak. However, bond length analysis indicates both Glu14 and Asp23 are protonated, which is supported by the continuous 2mFo − DFc electron density for CO bonds and broken density for C−O bonds in both instances.
Funding Information:
*E-mail: EPozharskiy@som.umaryland.edu. *E-mail: mwilson13@unl.edu. ORCID Mark A. Wilson: 0000-0001-6317-900X Funding This work was supported in part by National Institutes of Health Grant R01GM092999 to M.A.W. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, under Contract DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research and by the National Institutes of Health, National Institute of General Medical Sciences (NIGMS) (including Grant P41GM103393). This research used resources of the Advanced Photon Source, a DOE Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract DE-AC02-06CH11357. Use of BioCARS was also supported by the NIGMS via Grant R24GM111072. Notes The authors declare no competing financial interest.
PY - 2017
Y1 - 2017
N2 - Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donoracceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [O-O> = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.
AB - Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donoracceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [O-O> = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.
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U2 - 10.1021/acs.biochem.6b00906
DO - 10.1021/acs.biochem.6b00906
M3 - Article
C2 - 27989121
AN - SCOPUS:85020374593
VL - 56
SP - 391
EP - 402
JO - Biochemistry
JF - Biochemistry
SN - 0006-2960
IS - 2
ER -