Effects of Co-operative Ligand Binding on Protein Amide NH Hydrogen Exchange

Polshakov, Vladimir I.; Birdsall, B.; Feeney, J.

doi:10.1016/j.jmb.2005.11.084

Cited by 27 publications

(33 citation statements)

References 59 publications

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“…Clarifying such conformational motions at the level of the atom or residue is essential for understanding the structural stabilities of proteins and the relationships between protein structures and functions (3)(4)(5). The hydrogen/deuterium (H/D) 4 exchange of amide protons in backbones has become an important way to address the motions of a protein from small or relatively large scale motions involved in biological functions such as binding of a substrate or releasing a product to much more large scale motions like a global unfolding process (4,6). Among several approaches, the H/D exchange combined with heteronuclear NMR spectroscopy is the most convenient and powerful way because it can provide residue-specific information for most residues (7).…”

mentioning

confidence: 99%

“…Among several approaches, the H/D exchange combined with heteronuclear NMR spectroscopy is the most convenient and powerful way because it can provide residue-specific information for most residues (7). For many globular proteins, this approach has identified protected cores, which are often composed of secondary structures buried inside the molecules and the cooperative interactions with partner molecules (4,8), leading to allostery (9). Detailed analyses of exchanges in the native state of cytochrome c in the presence of various concentrations of denaturants suggested a pathway to unfolding, in which groups of secondary structural elements (i.e.…”

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confidence: 99%

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Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Lee

Tamura

Hoshino

et al. 2007

Journal of Biological Chemistry

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NMR-detected hydrogen/deuterium (H/D) exchange of amide protons is a powerful way for investigating the residuebased conformational stability and dynamics of proteins in solution. Maize ferredoxin-NADP ؉ reductase (FNR) is a relatively large protein with 314 amino acid residues, consisting of flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide phosphate (NADP ؉ )-binding domains. To address the structural stability and dynamics of FNR, H/D exchange of amide protons was performed using heteronuclear NMR at pD r values 8.0 and 6.0, physiologically relevant conditions mimicking inside of chloroplasts. At both pD r values, the exchange rate varied widely depending on the residues. The profiles of protected residues revealed that the highly protected regions matched well with the hydrophobic cores suggested from the crystal structure, and that the NADP ؉ -binding domain can be divided into two subdomains. The global stability of FNR obtained by H/D exchange with NMR was higher than that by chemical denaturation, indicating that H/D exchange is especially useful for analyzing the residue-based conformational stability of large proteins, for which global unfolding is mostly irreversible. Interestingly, more dynamic conformation of the C-terminal subdomain of the NADP ؉ -binding domain at pD r 8.0, the daytime pH in chloroplasts, than at pD r 6.0 is likely to be involved in the increased binding of NADP ؉ for elevating the activity of FNR. In light of photosynthesis, the present study provides the first structure-based relationship of dynamics with function for the FNR-type family in solution.Protein conformations as shown by x-ray crystallography or nuclear magnetic resonance spectroscopy are virtually dynamic entities over various time ranges in solution (1, 2). Clarifying such conformational motions at the level of the atom or residue is essential for understanding the structural stabilities of proteins and the relationships between protein structures and functions (3-5). The hydrogen/deuterium (H/D) 4 exchange of amide protons in backbones has become an important way to address the motions of a protein from small or relatively large scale motions involved in biological functions such as binding of a substrate or releasing a product to much more large scale motions like a global unfolding process (4, 6). Among several approaches, the H/D exchange combined with heteronuclear NMR spectroscopy is the most convenient and powerful way because it can provide residue-specific information for most residues (7). For many globular proteins, this approach has identified protected cores, which are often composed of secondary structures buried inside the molecules and the cooperative interactions with partner molecules (4, 8), leading to allostery (9). Detailed analyses of exchanges in the native state of cytochrome c in the presence of various concentrations of denaturants suggested a pathway to unfolding, in which groups of secondary structural elements (i.e. foldons) are unfolded sequentially through distin...

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confidence: 99%

mentioning

confidence: 99%

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Lee

Tamura

Hoshino

et al. 2007

Journal of Biological Chemistry

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“…Similarly, analysis of H/D exchange with neutron diffraction (ND) is a powerful tool for investigating dynamics (26,27). Recently, H/D exchange was used to study the structural fluctuations of various DHFR complexes by MS (28) and NMR (29). In the MS study on E. coli DHFR, the exchange of backbone amides in the Met-20 loop was fast, and Ϸ75% of the twisted eight-stranded ␤-sheet of apo DHFR was exchanged.…”

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confidence: 99%

“…However, ligand binding dampened the exchange rates (28). In the NMR study of Lactobacillus casei DHFR, changes in amide protection induced by ligand binding are not localized to specific binding sites but are extended throughout the entire structure by an intramolecular interaction network (29). With the ND structure of the DHFR⅐MTX complex, we are able compare the H/D exchange patterns between the occluded and closed conformers to probe loop dynamics.…”

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confidence: 99%

Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate

Bennett

Langan

Coates

et al. 2006

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

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“…It has been asserted that directionality of vibrations affects the substrate specificity, 58 and ligand induced protein conformational flexibility may be important in the co-operativity in the ligand binding. 59 The rotational domain motions we observe are possibly important in substrate/cofactor binding/releasing steps, because they have direct influence on the area and shape of the cofactor and substrate binding sites.…”

Section: Discussionmentioning

confidence: 84%

Effect of ligand binding on the intraminimum dynamics of proteins

Alakent¹,

Baskan²,

Doruker³

2010

J Comput Chem

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Effects of ligand binding on protein dynamics are studied via molecular dynamics (MD) simulations on two different enzymes, dihydrofolate reductase (DHFR) and triosephosphate isomerase (TIM), in their unliganded (free) and liganded states. Domain motions in MD trajectories are analyzed by collectivities and rotation angles along the principal components (PCs). DHFR in the free state has well-defined domain rotations, whereas rotations are slightly damped in the binary complex with nicotinamide adenine dinucleotide phosphate (NADPH), and remarkably distorted in the presence of NADP(+) , showing that NADP(+) is solely responsible for the loss of correlation of the domains in DHFR. Although mean square fluctuations of MD simulations in the same PC subspaces are similar for different ligation states, linear stochastic time series models show that backbone flexibility along the first five PCs is decreased upon NADPH and NADP(+) binding in subpicosecond scale. This shows that mobility of the protein along the PCs is closely related with intraminimum dynamics, and alterations in ligation states may change the intraminimum dynamics significantly. Low vibrational frequencies of the alpha-carbon atoms of DHFR are determined from the time series models of a larger number of low indexed PCs, and it is found that number of modes in the lowest frequencies is reduced upon ligand binding. A similar result is obtained for TIM in the unliganded and dihydroxyacetone phosphate bound states. We suggest that stochastic time series modeling is a promising method to be used in determining subtle perturbations in protein dynamics.

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Effects of Co-operative Ligand Binding on Protein Amide NH Hydrogen Exchange

Cited by 27 publications

References 59 publications

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate

Effect of ligand binding on the intraminimum dynamics of proteins

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