Effects of Calcium Binding on the Side-chain Methyl Dynamics of Calbindin D9k: A 2H NMR Relaxation Study

Johnson, Eric; Chazin, Walter J.; Rance, Mark

doi:10.1016/j.jmb.2006.01.031

Cited by 18 publications

(32 citation statements)

References 64 publications

(97 reference statements)

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“…This is consistent with the observed S-NO-induced exposure of aromatic residues, which must lead to different hydration of the protein. The loss of side-chain entropy due to formation of a more rigid linker loop most probably leads to enhanced flexibility of other protein regions, as previously observed during calcium binding to calbindin D 9k (70). It is worth noting that S-NO-induced elongation of the helical element in the hinge region shown in this study for homodimeric apo-S100A1 resembles that described for the monomeric calbindin D 9k mutant P43MG (71).…”

Section: Discussionsupporting

confidence: 81%

Post-translational S-Nitrosylation Is an Endogenous Factor Fine Tuning the Properties of Human S100A1 Protein

Živković

Zaręba-Kozioł

Zhukova

et al. 2012

Journal of Biological Chemistry

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Background: S100A1 protein is a proposed target of molecule-guided therapy for heart failure. Results: S-Nitrosylation of S100A1 is present in cells, increases Ca 2ϩ binding, and tunes the overall protein conformation. Conclusion: Thiol-aromatic molecular switch is responsible for NO-related modification of S100A1 properties. Significance: Post-translational S-nitrosylation may provide functional diversity and specificity to S100A1 and other S100 protein family members.

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Section: Discussionsupporting

confidence: 81%

Post-translational S-Nitrosylation Is an Endogenous Factor Fine Tuning the Properties of Human S100A1 Protein

Živković

Zaręba-Kozioł

Zhukova

et al. 2012

Journal of Biological Chemistry

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“…In contrast, data for Leu6, 30, 46 and 69 required a reduced effective rotational correlation time in the fitting. As described for other proteins [12,14,26] this is the hallmark of rotameric transitions taking place on a time scale comparable to molecular reorientation. The pres- Figure 3.…”

mentioning

confidence: 63%

“…[25] These data are very similar to those A C H T U N G T R E N N U N G determined for the P43M mutant of the same protein. [26] The presence of averaging about axes between the methyl group and the backbone on the subnanosecond time scale is expected to lead to reduced order parameters, and inconsistency with simple motional models that account for internal correlation functions that decay on the picosecond time scale exclusively. [12] A two-parameter fit with a high methyl axis order parameter was obtained for Leu23 and Leu28 and is indicative of the absence of rotameric transitions.…”

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confidence: 99%

Leucine Side‐Chain Conformation and Dynamics in Proteins from ¹³C NMR Chemical Shifts

Mulder

2009

ChemBioChem

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The g-gauche effect in 13 C NMR spectroscopy refers to the magnetic nonequivalence of the methyl carbons of the terminal isopropyl groups that are attached to branched alkanes; [1][2][3] this effect results in magnetic shielding of the carbon nucleus of the substituent in the gauche position by about 5 ppm relative to that of the same chemical group in the trans position. [4][5][6] Tonelli and colleagues demonstrated that the 13 C chemical shift of a carbon nucleus in a particular polymer stereoisomer is attributable solely to stereosequence-dependent differences in the probability that the given carbon atom is A C H T U N G T R E N N U N G involved in three-bond gauche interactions with other heavy atoms. Through this simple observation they were able to accurately and quantitatively predict the experimental 13 C NMR spectra of polypropylene and polypropylene model compounds with different stereoregularities. [4,5,7,8] We demonstrate here the use of the 13 C NMR g-gauche effect to establish leucine rotamer conformations in proteins, and provide a quantitative measure of their dynamics. This information is of value as a restraint on side-chain conformation in protein structure model building, [9,10] and is highly valuable for the interpretation of side chain methyl dynamics from 2 H or 13 C nuclear spin relaxation. [11][12][13][14][15][16] Although we focus below on methyl groups of leucine (Leu) residues, the g-gauche effect is a general determinant of chemical shifts of amino acid side-chain carbon nuclei, and expected to play an import role in their conformational analysis. [17][18][19] Leucine side chains can assume three stable staggered conformations of lowest potential energy as a function of the dihedral angle c 2 , referred to [20] as gauche(+) or p, gauche(À) or m, and trans or t (Figure 1). A carbon, rather than a proton, substituent in the gauche position leads to high internal energy, and results in the prevalence of conformations in which one atom is trans to the Ca atom, while the remaining atom is positioned gauche. Consequently, the two dominant c 2 rotamers are t and p. The energetics are mirrored by the c 2 side-chain distributions found in protein crystal structures. [20,21] In fact, at ambient temperature a small preference (2:1) of t over p is noticed in protein structures, as is observed for branched alkanes. [7] An analysis of the stereospecifically assigned methyl 13 C chemical shifts in the BioMagResBank (http://www.bmrb.wisc.edu/) is shown in Figure 2. The NMR data show that the preference of t over p observed in crystalline proteins is perfectly mirrored in solution.We have previously noted a strong correlation between the 3 J CC coupling and the methyl carbon chemical shift difference for leucine residues in two proteins; [22] this suggests that the wide distribution seen in Figure 2 could result from rotameric interconversion about the c 2 dihedral angle. A recent report by London and co-workers [19] supports this conclusion, and demonstrates that correlations between NMR side chain ...

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“…NMR isotropic chemical shifts and chemical shift anisotropy are widely used to characterize the structure and dynamics of guest species in inclusion compounds [11,13,14,[22][23][24][25][26][27][28][29][30][31][32][33][34][35] and functional groups in solids. [36][37][38] A comparison of the chemical shift of the guest in the inclusion compound with the free guest can give an indication of the encapsulation of the guest in the cages of the system. Peak integration of the guests, along with knowledge of the structure and number of different cages in the inclusion compound, allows for the assignment of peaks in the NMR spectrum to guests in different cages.…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, the method is general and can be used to predict chemical shift anisotropies of pure solid phases with dynamically disordered components or of dynamically mobile side-chains of protein molecules as well. [36][37][38] …”

Section: Introductionmentioning

confidence: 99%

Determination of NMR Lineshape Anisotropy of Guest Molecules within Inclusion Complexes from Molecular Dynamics Simulations

2008

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Nonspherical cages in inclusion compounds can result in non-uniform motion of guest species in these cages and anisotropic lineshapes in NMR spectra of the guest. Herein, we develop a methodology to calculate lineshape anisotropy of guest species in cages based on molecular dynamics simulations of the inclusion compound. The methodology is valid for guest atoms with spin 1/2 nuclei and does not depend on the temperature and type of inclusion compound or guest species studied. As an example, the nonspherical shape of the structure I (sI) clathrate hydrate large cages leads to preferential alignment of linear CO(2) molecules in directions parallel to the two hexagonal faces of the cages. The angular distribution of the CO(2) guests in terms of a polar angle theta and azimuth angle phi and small amplitude vibrational motions in the large cage are characterized by molecular dynamics simulations at different temperatures in the stability range of the CO(2) sI clathrate. The experimental (13)C NMR lineshapes of CO(2) guests in the large cages show a reversal of the skew between the low temperature (77 K) and the high temperature (238 K) limits of the stability of the clathrate. We determine the angular distributions of the guests in the cages by classical MD simulations of the sI clathrate and calculate the (13)C NMR lineshapes over a range of temperatures. Good agreement between experimental lineshapes and calculated lineshapes is obtained. No assumptions regarding the nature of the guest motions in the cages are required.

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Effects of Calcium Binding on the Side-chain Methyl Dynamics of Calbindin D9k: A 2H NMR Relaxation Study

Cited by 18 publications

References 64 publications

Post-translational S-Nitrosylation Is an Endogenous Factor Fine Tuning the Properties of Human S100A1 Protein

Post-translational S-Nitrosylation Is an Endogenous Factor Fine Tuning the Properties of Human S100A1 Protein

Leucine Side‐Chain Conformation and Dynamics in Proteins from ¹³C NMR Chemical Shifts

Determination of NMR Lineshape Anisotropy of Guest Molecules within Inclusion Complexes from Molecular Dynamics Simulations

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Effects of Calcium Binding on the Side-chain Methyl Dynamics of Calbindin D9k: A 2H NMR Relaxation Study

Cited by 18 publications

References 64 publications

Post-translational S-Nitrosylation Is an Endogenous Factor Fine Tuning the Properties of Human S100A1 Protein

Post-translational S-Nitrosylation Is an Endogenous Factor Fine Tuning the Properties of Human S100A1 Protein

Leucine Side‐Chain Conformation and Dynamics in Proteins from 13C NMR Chemical Shifts

Determination of NMR Lineshape Anisotropy of Guest Molecules within Inclusion Complexes from Molecular Dynamics Simulations

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Leucine Side‐Chain Conformation and Dynamics in Proteins from ¹³C NMR Chemical Shifts