The determinants of carboxyl pK<sub>a</sub> values in turkey ovomucoid third domain

Li, Hui; Robertson, Andrew D.; Jensen, Jan H.

doi:10.1002/prot.20032

Cited by 100 publications

(119 citation statements)

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“…Our titrations reveal the additive nature of the effect of zeaxanthin and PsbS on the pK a of protonable residues associated with qE. The apparent pK a of amino acids has been shown to strongly depend upon their environment (55)(56)(57). Hydrogen bonding, steric hindrance, and the di-electric constant of the environment can all affect the pK a of amino acids (55)(56)(57).…”

Section: Methodsmentioning

confidence: 72%

“…The apparent pK a of amino acids has been shown to strongly depend upon their environment (55)(56)(57). Hydrogen bonding, steric hindrance, and the di-electric constant of the environment can all affect the pK a of amino acids (55)(56)(57). For instance the pK a of the carboxyl group on aspartate can be as low as 2.4 when exposed to water due to hydrogen bonding, whereas in hydrophobic environments the pK a can be as high as 6.4 (56).…”

Section: Methodsmentioning

confidence: 99%

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Restoration of Rapidly Reversible Photoprotective Energy Dissipation in the Absence of PsbS Protein by Enhanced ΔpH

Johnson

Ruban

2011

Journal of Biological Chemistry

119

105

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Variations in the light environment require higher plants to regulate the light harvesting process. Under high light a mechanism known as non-photochemical quenching (NPQ) is triggered to dissipate excess absorbed light energy within the photosystem II (PSII) antenna as heat, preventing photodamage to the reaction center. The major component of NPQ, known as qE, is rapidly reversible in the dark and dependent upon the transmembrane proton gradient (⌬pH), formed as a result of photosynthetic electron transport. Using diaminodurene and phenazine metasulfate, mediators of cyclic electron flow around photosystem I, to enhance ⌬pH, it is demonstrated that rapidly reversible qE-type quenching can be observed in intact chloroplasts from Arabidopsis plants lacking the PsbS protein, previously believed to be indispensible for the process. The qE in chloroplasts lacking PsbS significantly quenched the level of fluorescence when all PSII reaction centers were in the open state (F o state), protected PSII reaction centers from photoinhibition, was modulated by zeaxanthin and was accompanied by the qEtypical absorption spectral changes, known as ⌬A 535 . Titrations of the ⌬pH dependence of qE in the absence of PsbS reveal that this protein affects the cooperativity and sensitivity of the photoprotective process to protons. The roles of PsbS and zeaxanthin are discussed in light of their involvement in the control of the proton-antenna association constant, pK, via regulation of the interconnected phenomena of PSII antenna reorganization/aggregation and hydrophobicity.Sunlight can fluctuate frequently and dramatically in both intensity and spectral quality during the day. The photosynthetic membrane of higher plants has evolved to operate efficiently under such light conditions. In shade, large arrays of antenna complexes efficiently harvest and deliver photon energy to the photochemical reaction centers for use in photosynthesis. In high light the membrane switches to a photoprotective state where the excess absorbed energy, which has the potential to cause damage, is safely dissipated as heat (1, 2). The amount of energy dissipation can be monitored by the nonphotochemical quenching of chlorophyll fluorescence (NPQ) 2 (1, 2). The major component of NPQ, qE, is rapidly reversible in the dark and is dependent upon the level of the transmembrane proton gradient (⌬pH). ⌬pH acts as a feedback signal indicating the degree of saturation of photosynthetic electron transport (1, 2). ⌬pH can be generated by linear electron flow (LEF), which involves the oxidation of water by photosystem II (PSII) and the transfer of electrons to NADP ϩ via the cytochrome b 6 f and photosystem I (PSI) complexes (3). In addition, cyclic electron flow (CEF), which involves the transfer of electrons in a closed loop around cytochrome b 6 f and PSI was reported to contribute to ⌬pH (4 -6). The contribution of CEF to ⌬pH generation is essential for maintaining the correct ATP/ NADPH ratio for CO 2 fixation in the chloroplast stroma (6). Imbalance in the AT...

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Section: Methodsmentioning

confidence: 72%

Section: Methodsmentioning

confidence: 99%

Restoration of Rapidly Reversible Photoprotective Energy Dissipation in the Absence of PsbS Protein by Enhanced ΔpH

Johnson

Ruban

2011

Journal of Biological Chemistry

119

105

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“…The correct prediction of protein titration states is important for the analysis of enzyme mechanisms, protein stability, and molecular recognition. As mentioned earlier, efforts have been underway for more than 80 years (Linderström-Lang, 1924;Antosiewicz et al, 1996b;Bastyns et al, 1996;Luo et al, 1998;Nielsen and Vriend, 2001;Fitch et al, 2002;Georgescu et al, 2002;Li et al, 2002;Alexov, 2003;Nielsen and McCammon, 2003;Li et al, 2004;Jensen et al, 2005;Krieger et al, in press) to correctly predict protein titration states and understand the determinants of pK a s for amino acids in protein environments (see chapter by Whitten, et al in this volume).…”

Section: Ive Pk a Calculationsmentioning

confidence: 99%

Computational Methods for Biomolecular Electrostatics

Dong

Olsen

Baker

2008

Methods in Cell Biology

116

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An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der Waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems with a particular focus on how computational tools can be used to investigate these types of interactions.

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“…The pK a value of S295 may be perturbed by the interaction of its O γ atom with the backbone NH groups of T297 and M298. 35,36 While the precise details surrounding the activation of S295 remain unclear and the involvement of serine in base catalysis uncommon given its intrinsically high pK a value, serine has been reported to play this role in other enzymes. 37 In line with our proposal is the increase in specific activity observed at pH 8.5 for ec-ADL, which would certainly be expected if S295 acts as the base catalyst.…”

Section: Role Of S295 In Base Catalysismentioning

confidence: 99%

Substrate and Product Complexes of Escherichia coli Adenylosuccinate Lyase Provide New Insights into the Enzymatic Mechanism

Tsai

Koo

et al. 2007

Journal of Molecular Biology

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Adenylosuccinate lyase (ADL) catalyzes the breakdown of 5-aminoimida-zole-(Nsuccinylocarboxamide) ribotide (SAICAR) to 5-aminoimidazole-4-carboxamide ribotide (AICAR) and fumarate, and of adenylosuccinate (ADS) to adenosine monophosphate (AMP) and fumarate in the de novo purine biosynthetic pathway. ADL belongs to the argininosuccinate lyase (ASL)/ fumarase C superfamily of enzymes. Members of this family share several common features including: a mainly α-helical, homotetrameric structure; three regions of highly conserved amino acid residues; and a general acid-base catalytic mechanism with the overall β-elimination of fumarate as a product. The crystal structures of wild-type Escherichia coli ADL (ec-ADL), and mutant-substrate (H171A-ADS) and -product (H171N-AMP•FUM) complexes have been determined to 2.0, 1.85, and 2.0 Å resolution, respectively. The H171A-ADS and H171N-AMP•FUM structures provide the first detailed picture of the ADL active site, and have enabled the precise identification of substrate binding and putative catalytic residues. Contrary to previous suggestions, the ec-ADL structures implicate S295 and H171 in base and acid catalysis, respectively. Furthermore, structural alignments of ec-ADL with other superfamily members suggest for the first time a large conformational movement of the flexible C3 loop (residues 287-303) in ec-ADL upon substrate binding and catalysis, resulting in its closure over the active site. This loop movement has been observed in other superfamily enzymes, and has been proposed to be essential for catalysis. The ADL catalytic mechanism is re-examined in light of the results presented here.

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The determinants of carboxyl pK_a values in turkey ovomucoid third domain

Cited by 100 publications

References 82 publications

Restoration of Rapidly Reversible Photoprotective Energy Dissipation in the Absence of PsbS Protein by Enhanced ΔpH

Restoration of Rapidly Reversible Photoprotective Energy Dissipation in the Absence of PsbS Protein by Enhanced ΔpH

Computational Methods for Biomolecular Electrostatics

Substrate and Product Complexes of Escherichia coli Adenylosuccinate Lyase Provide New Insights into the Enzymatic Mechanism

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The determinants of carboxyl pKa values in turkey ovomucoid third domain

Cited by 100 publications

References 82 publications

Restoration of Rapidly Reversible Photoprotective Energy Dissipation in the Absence of PsbS Protein by Enhanced ΔpH

Restoration of Rapidly Reversible Photoprotective Energy Dissipation in the Absence of PsbS Protein by Enhanced ΔpH

Computational Methods for Biomolecular Electrostatics

Substrate and Product Complexes of Escherichia coli Adenylosuccinate Lyase Provide New Insights into the Enzymatic Mechanism

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The determinants of carboxyl pK_a values in turkey ovomucoid third domain