Hydrogen Bonding and Chemical Reactivity

Hibbert, Frank; Emsley, John

doi:10.1016/s0065-3160(08)60047-7

Cited by 482 publications

(640 citation statements)

References 359 publications

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“…(4) The hydrogen bond between an Asp carboxylate oxygen and a phosphate oxygen, which is extremely short (2.432 A distance) as established in the ultra-high resolution structures, confers the exquisite specificity of the PBP and the phosphate transport system. Although the distance is within the proposed range of low barrier hydrogen bonds with estimated energies of 12-24 kcal/mol (Hibbert & Emsley, 1990;Cleland & Kreevoy, 1994). the contribution of the short hydrogen bond to the phosphate binding affinity is no better than that of a normal hydrogen bond.…”

mentioning

confidence: 63%

Dominant role of local dipolar interactions in phosphate binding to a receptor cleft with an electronegative charge surface: Equilibrium, kinetic, and crystallographic studies

et al. 1998

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Stringent specificity and complementarity between the receptor, a periplasmic phosphate-binding protein (PBP) with a two-domain structure, and the completely buried and dehydrated phosphate are achieved by hydrogen bonding or dipolar interactions. We recently found that the surface charge potential of the cleft between the two domains that contains the anion binding site is intensely electronegative. This novel finding prompted the study reported here of the effect of ionic strength on the equilibrium and rapid kinetics of phosphate binding.

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confidence: 63%

Dominant role of local dipolar interactions in phosphate binding to a receptor cleft with an electronegative charge surface: Equilibrium, kinetic, and crystallographic studies

et al. 1998

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“…Based on prior linear free energy studies and known physical properties of hydrogen bonds (8,17,(30)(31)(32)(33)(34)(35), we posited that energetic changes in the phenol-Y16 hydrogen bond with increasing phenol pK a would alter the stability of the Y16 anion, and thus modulate its ability to ionize relative to Y57. To account for this effect, we modified our equilibrium proton transfer model to allow the proton affinity of the Y16 anion to vary linearly with that of the phenol (modified expressions are shown in Materials and Methods, with additional discussion provided in SI Materials and Methods).…”

Section: Quantitative Modeling Of Ionization States Within the Ksi Hymentioning

confidence: 99%

“…Extensive prior hydrogen bond studies in small molecules provide strong evidence that increasing the pK a of a phenol or other hydrogen bond donor (via substituent effects) weakens its ability to donate a hydrogen bond to a common acceptor of lower pK a (17,18,32,34,60,61) due, in part, to the decrease in positive charge character of the hydroxylic proton and its weaker interaction with an anionic acceptor (17,60). Increasing phenol pK a is also expected to lengthen the hydrogen bond to the Y16 anion as the proton affinities of the two groups become increasingly mismatched (8), reducing charge-transfer across the hydrogen bond and increasing negative charge localization on the Y16 anion (30,31). These changes, which progressively weaken the phenol-Y16 hydrogen bond, destabilize the Y16 anion and thereby favor formation of the Y57 anion instead, which is stabilized by hydrogen bonds from Y16 and Y32 (Fig.…”

Section: Electrostatic Effects Of Charge Rearrangement Within the Actmentioning

confidence: 99%

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

Sigala¹,

Fafarman²,

Schwans³

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated sitespecific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol-Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations.computational modeling | enzyme catalysis | protein electrostatics | protein semisynthesis | active site environment H ydrogen bond networks are ubiquitous structural features within proteins, and they play key roles linking secondary and tertiary structural elements and spanning protein-protein interfaces. Such networks are especially common within enzyme active sites, where they position protein and substrate groups for catalysis, stabilize charge rearrangements during chemical transformations, and mediate proton transfers (1). Despite the prevalence and critical structural and functional roles of hydrogen bond networks, incisive dissection of their physical properties within the idiosyncratic interior of folded proteins remains difficult.Hydrogen-bonded protons are not observed in the vast majority of protein X-ray structures due to the low X-ray scattering power of hydrogen atoms (2). Thus, the presence of hydrogen bond networks is typically inferred from the proximity and orientation of hydrogen bond donor and acceptor groups within refined protein structural models. The inherent inability of most X-ray diffraction studies to monitor proton positions imposes additional challenges for dissecting the physical features that influence the equilibrium protonation states of specific residues along a hydrogen-bonded proton transfer network. Furthermore, it remains extremely challenging t...

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“…:-state hemoglobins (BC 112G and B(C93A,C 112G)) at 2.0 and 1.8 A resolution, respectively, are reported along with the three-dimensional structure of R-state carbonmonoxy-hemoglobin at 2.2 A resolution. The structures have been solved by The higher resolution structure has extensive solvent structure, including a sulfate binding site between both the cx1B2 and the 0'.2B1 subunits, and has Fe-C-0 angles of 125" and 162° for the ex and 13 subunits, respectively, that differ from the angles previously reported in the lower resolution crystallographic study (Baldwin, 1980), however are nearer to the angles determined for myoglobin crystallographically (Kmijan, et al, 1 , et al 1993. PDB: 1osa).…”

mentioning

confidence: 82%

What is the structural basis for the coupling of Ca²⁺and peptide binding by calmodulin?

Weigand¹,

Mirzoeva²,

Shuvalova³

et al. 1996

Acta Cryst Sect A

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Hydrogen Bonding and Chemical Reactivity

Cited by 482 publications

References 359 publications

Dominant role of local dipolar interactions in phosphate binding to a receptor cleft with an electronegative charge surface: Equilibrium, kinetic, and crystallographic studies

Dominant role of local dipolar interactions in phosphate binding to a receptor cleft with an electronegative charge surface: Equilibrium, kinetic, and crystallographic studies

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

What is the structural basis for the coupling of Ca²⁺and peptide binding by calmodulin?

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Hydrogen Bonding and Chemical Reactivity

Cited by 482 publications

References 359 publications

Dominant role of local dipolar interactions in phosphate binding to a receptor cleft with an electronegative charge surface: Equilibrium, kinetic, and crystallographic studies

Dominant role of local dipolar interactions in phosphate binding to a receptor cleft with an electronegative charge surface: Equilibrium, kinetic, and crystallographic studies

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

What is the structural basis for the coupling of Ca2+and peptide binding by calmodulin?

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What is the structural basis for the coupling of Ca²⁺and peptide binding by calmodulin?