Ion Binding in Biological Systems as Studied by NMR Spectroscopy

Forsén, Sture; Lindman, Björn

doi:10.1002/9780470110478.ch5

Cited by 101 publications

(4 citation statements)

References 377 publications

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“…The measured fast and the slow T 2 relaxation times were: T 2f tiss= 2.2 ms and T 2s tiss= 20.4 ms, respectively, and T 1 tiss = 34 ms. The relaxation times of the standard saline reference were T 1 std = T 2 std = 60 ms [27].…”

Section: In Vivo Mrimentioning

confidence: 99%

Functional sodium magnetic resonance imaging of the intact rat kidney

Maril¹,

Margalit²,

Mispelter³

et al. 2004

Kidney International

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Section: In Vivo Mrimentioning

confidence: 99%

Functional sodium magnetic resonance imaging of the intact rat kidney

Maril¹,

Margalit²,

Mispelter³

et al. 2004

Kidney International

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“…Ion binding is central to nearly all biological processes, , but the structural dynamics and energy exchange characteristics of ion coordination events in proteins remain incompletely understood. , Similarly, the complete sequences of structural changes induced by ion binding in proteins and culminating in signal transduction or other biochemical action are, in most cases, not known. − While it is unlikely that all processes occurring on picometer/picosecond scales are critical to biomolecular events, measurements in these regimes, beyond the resolution of widely used structural methods such as NMR spectroscopy and X-ray crystallography, − nonetheless contain useful information about slower, unquestionably important processes. As we will show, vibrational relaxation which proceeds in hundreds of femtoseconds reflects miniscule ion-dependent changes in equilibrium binding structure that modulate the anharmonic couplings between vibrational modes.…”

Section: Introductionmentioning

confidence: 99%

Vibrational Relaxation in EDTA Is Ion-Dependent

Edington

Baiz

2018

J. Phys. Chem. A

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Ion binding by carboxylate groups is common in biomolecules such as metalloproteins, but dynamical aspects of ion binding are not fully understood. We present ultrafast spectroscopic measurements of vibrational relaxation in the ion-coordinating carboxylate groups of EDTA, which we use as a model of carboxylate-mediated ion binding, as EDTA binds a series of divalent and trivalent metal ions with high affinity. The measurements are interpreted using a Redfield-based anharmonic model of vibrational relaxation that rationalizes trends in vibrational lifetimes in terms of vibrational energy transfer between EDTA's asymmetric carboxylate stretching vibrational modes and lower-lying modes. Results show ion-dependent changes in complex structure and dynamics well outside the temporal and spatial resolution of common structural methods and demonstrate how vibrational relaxation measurements may contribute to exploration of ion-binding dynamics on ultrashort length and time scales.

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“…Structural and functional descriptions of the important process of ion binding to proteins remain incomplete. − This difficulty is partly due to the fact that clear observables marking site-dependent occupancy and ion-dependent conformational changes are often unavailable or difficult to interpret. Site-specific mutagenesis provides the tools needed to engineer useful observables into ion binding proteins, thus facilitating the characterization of binding processes.…”

mentioning

confidence: 99%

Non-Additive Effects of Binding Site Mutations in Calmodulin

et al. 2019

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Despite decades of research on ion-sensing proteins, gaps persist in the understanding of ion binding affinity and selectivity even in well-studied proteins such as calmodulin. Site-directed mutagenesis is a powerful and popular tool for addressing outstanding questions about biological ion binding and is employed to selectively deactivate binding sites and insert chromophores at advantageous positions within ion binding structures. However, even apparently nonperturbative mutations can distort the binding dynamics they are employed to measure. We use Fourier transform infrared (FTIR) and ultrafast two-dimensional infrared (2D IR) spectroscopy of the carboxylate asymmetric stretching mode in calmodulin as a mutation-and label-independent probe of the conformational perturbations induced in calmodulin's binding sites by two classes of mutation, tryptophan insertion and carboxylate side-chain deletion, commonly used to study ion binding in proteins. Our results show that these mutations not only affect ion binding but also induce changes in calmodulin's conformational landscape along coordinates not probed by vibrational spectroscopy, remaining invisible without additional perturbation of binding site structure. Comparison of FTIR line shapes with 2D IR diagonal slices provides a clear example of how nonlinear spectroscopy produces well-resolved line shapes, refining otherwise featureless spectral envelopes into more informative vibrational spectra of proteins.

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Ion Binding in Biological Systems as Studied by NMR Spectroscopy

Cited by 101 publications

References 377 publications

Functional sodium magnetic resonance imaging of the intact rat kidney

Functional sodium magnetic resonance imaging of the intact rat kidney

Vibrational Relaxation in EDTA Is Ion-Dependent

Non-Additive Effects of Binding Site Mutations in Calmodulin

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