Low-frequency localized spin-dynamical coupling in proteins

Korb, Jean-Pierre; Van-Quynh, A.; Bryant, Robert G.

doi:10.1016/s1387-1609(01)01323-8

Cited by 8 publications

(8 citation statements)

References 21 publications

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“…Previous MRD studies of dry proteins have shown that the relaxation is described by a power law in the Larmor frequency,

\frac{1}{T_{1}} = A ω^{- b}

, where A and b are constants [5; 6; 7; 8; 9; 10]. The physical origin of the power law has been related to a spin-fracton relaxation mechanism [6; 11; 12; 13; 14; 15].…”

Section: Introductionmentioning

confidence: 99%

“…The essential dynamical picture behind this relaxation mechanism is similar to those employed in vibrational network models for protein dynamics [16; 17; 18]. The propagation of structural fluctuations in the protein which modulate 1 H dipolar couplings that drive spin relaxation are characterized by a reduced dimensionality because of the limited or non-uniform connectivity in the folded protein structure [6; 7; 19]. The exponent, b , in the power law is related by the relaxation theory to a spectral dimension, d s , which characterizes the vibrational density of states and the dimensionality of the disturbance propagation, and a fractal dimension, d f , which describes the distribution of mass in space [6].…”

Section: Introductionmentioning

confidence: 99%

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Water molecule contributions to proton spin–lattice relaxation in rotationally immobilized proteins

Goddard

Korb

Bryant

2009

Journal of Magnetic Resonance

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Spin-lattice relaxation rates of protein and water protons in dry and hydrated immobilized bovine serum albumin were measured in the range of 1H Larmor frequency from 10 kHz to 30 MHz at temperatures from 154 to 302 K. The water proton spin-lattice relaxation reports on that of protein protons, which causes the characteristic power law dependence on the magnetic field strength. Isotope substitution of deuterium for hydrogen in water and studies at different temperatures expose three classes of water molecule dynamics that contribute to the spin-lattice relaxation dispersion profile. At 185 K, a water 1H relaxation contribution derives from reorientation of protein-bound molecules that are dynamically uncoupled from the protein backbone and is characterized by a Lorentzian function. Bound water molecule motions that can be dynamically uncoupled or coupled to the protein fluctuations make dominant contributions at higher temperatures as well. Surface water translational diffusion that is magnetically two-dimensional makes relaxation contributions at frequencies above 10 MHz. It is shown using isotope substitution that the exponent of the power law of the water signal in hydrated immobilized protein systems is the same as that for protons in lyophilized proteins over four orders of magnitude in the Larmor frequency, which implies that changes in the protein structure associated with hydration do not affect the 1H spin relaxation.

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“…Previous MRD studies of dry proteins have shown that the relaxation is described by a power law in the Larmor frequency,

\frac{1}{T_{1}} = A ω^{- b}

, where A and b are constants [5; 6; 7; 8; 9; 10]. The physical origin of the power law has been related to a spin-fracton relaxation mechanism [6; 11; 12; 13; 14; 15].…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Water molecule contributions to proton spin–lattice relaxation in rotationally immobilized proteins

Goddard

Korb

Bryant

2009

Journal of Magnetic Resonance

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“…The interpretation of these measurements is built on a quantum theory of the nuclear spin relaxation induced by time fluctuations of the proton dipole-dipole interaction, H dip (t), between spins in a disordered or non-crystalline solid (17)(18)(19)(20)(21). This interaction is expanded as a superposition of pairwise contributions H dip ðtÞ ¼ + i,j H dip i;j ½r ij ðtÞ; u ij ðtÞ; which depends mainly on the interspin distance r ij (t) and the angle u ij (t) between r ij and the constant magnetic field B 0 .…”

Section: Theorymentioning

confidence: 99%

Noise and Functional Protein Dynamics

Korb

Bryant

2005

Biophysical Journal

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The magnetic field dependence of the proton-spin-lattice relaxation rate in rotationally immobilized proteins shows that the one-dimensional character of the protein primary structure causes a dramatic increase in the population of low-frequency motions from 10 kHz to 20 MHz. As a consequence, the probability and rate at which functionally critical conformational states are thermally sampled in a protein are dramatically increased as well, when compared with a three-dimensional lattice structure. Studies of protein dynamics often focus on time periods far shorter than those associated with catalytic function, but we show here that the magnetic field dependence of the proton nuclear spin-lattice relaxation rate in rotationally immobilized proteins reports unambiguously the structural fluctuations in the frequency range from 10 kHz to 20 MHz. This relaxation rate decreases with increasing Larmor frequency according to a power law that derives from the distribution of dynamical states, the localization of the structural disturbances, and the spatial distribution of hydrogen atoms in the structure. The robust theoretical foundation for the spin-relaxation process, loosely characterized as a direct spin-phonon coupling, shows that the disturbances propagate in a space of reduced dimensionality, essentially along the stiff connections of the polypeptide chain. The reduced dimensionality traps the disturbance and changes the efficiency for energy redistribution in the protein and the processes that drive nuclear spin relaxation. We also show that the Larmor frequency dependence of the protein-proton-spin-lattice relaxation rate constant is related to the frequency dependence of force constants and mean-square displacement commonly observed or calculated for proteins. We believe that these approaches give additional physical insight into the character of the extremely low-frequency protein dynamics.

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“…This profile is a quantitative measurement of molecular dynamics occurring on timescales of ms to ns within the material under study, providing unique insights on tissue structure non-invasively. NMR relaxometry has been intensively expanding in recent years, offering interesting applications in physics and chemistry for liquid 11 – 13 , macromolecular (polymers, proteins) 6 , 11 , 13 – 15 and solid state systems 16 – 19 , including the possibility of modelling the relaxation enhancement for paramagnetic contrast agents 20 – 22 . Relaxation dispersion profiles for protein systems also show frequency-specific relaxation maxima, referred to as quadrupole peaks 23 – 26 , an effect referred to as Quadrupole Relaxation Enhancement (QRE) 16 – 19 , 23 – 28 , the physical origin of which is well understood 16 , 27 , 28 .…”

Section: Introductionmentioning

confidence: 99%

Towards applying NMR relaxometry as a diagnostic tool for bone and soft tissue sarcomas: a pilot study

Masiewicz

Ashcroft

Boddie

et al. 2020

Sci Rep

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This work explores what Fast Field-Cycling Nuclear Magnetic Resonance (FFC-NMR) relaxometry brings for the study of sarcoma to guide future in vivo analyses of patients. We present the results of an ex vivo pilot study involving 10 cases of biopsy-proven sarcoma and we propose a quantitative method to analyse 1 H NMR relaxation dispersion profiles based on a model-free approach describing the main dynamical processes in the tissues and assessing the amplitude of the Quadrupole Relaxation Enhancement effects due to 14 N. This approach showed five distinct groups of dispersion profiles indicating five discrete categories of sarcoma, with differences attributable to microstructure and rigidity. Data from tissues surrounding sarcomas indicated very significant variations with the proximity to tumour, which may be attributed to varying water content but also to tissue remodelling processes due to the sarcoma. This pilot study illustrates the potential of FFC relaxometry for the detection and characterisation of sarcoma. Magnetic Resonance Imaging (MRI) is a powerful method used in the medical diagnosis of a range of different soft tissue pathologies. The principle of MRI lies in detecting differences in the behaviour of nuclear spins (in most cases from 1 H) between pathological tissues and their healthy counterparts, which can be exploited as a source of contrast to form images. Spin-lattice and spin-spin relaxation times, denoted as T 1 and T 2 respectively, are two important sources of MRI contrast that describe how fast tissues return to magnetic equilibrium after excitation. To simplify calculations one often uses their reciprocal values, R 1 = 1/T 1 and R 2 = 1/T 2 , which are referred to as spin-lattice and spin-spin relaxation rates, respectively 1-3 but convey the same information. R 1 usually shows much better contrast at fields below 0.5 T but most clinical scanners operate at 1.5 T or 3 T to achieve high spatial resolution. Paramagnetic contrast agents are commonly used to improve contrast 4,5 , providing relaxation enhancement caused by strong magnetic dipole-dipole interactions between protons (hydrogen nuclei, 1 H) from the tissues and the paramagnetic centre (typically gadolinium or manganese ions). Despite the huge progress in advanced contrast agents and MRI technology, the early diagnosis and treatment of patients with musculoskeletal (MSK) malignancies (sarcomas) remains a major challenge. Initial detection of MSK malignancies depends upon clinical examination, fine needle aspiration cytology or core biopsy and MRI. MRI is also used in the follow-up and surveillance of patients with suspected local recurrence following treatment. Unfortunately, the imaging characteristics of tissues using conventional MRI are not diagnostic for a large number of soft tissue tumours and therefore careful multidisciplinary interpretation of the combined results are required in reaching a final diagnosis. Despite this, it can still be challenging to estimate tumour aggressiveness or resection margins.

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Low-frequency localized spin-dynamical coupling in proteins

Cited by 8 publications

References 21 publications

Water molecule contributions to proton spin–lattice relaxation in rotationally immobilized proteins

Water molecule contributions to proton spin–lattice relaxation in rotationally immobilized proteins

Noise and Functional Protein Dynamics

Towards applying NMR relaxometry as a diagnostic tool for bone and soft tissue sarcomas: a pilot study

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