Orientational ordering and dynamics of the hydrate and exchangeable hydrogen atoms in crystalline crambin

Usha, M.G.; Wittebort, Richard J.

doi:10.1016/0022-2836(89)90157-5

Cited by 49 publications

(56 citation statements)

References 28 publications

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“…The largest contributors to these fluctuations are residues 1 and 33-39. These residues belong to beta sheet regions (residues 1-4 and [32][33][34][35] and to coil regions (residues [36][37][38][39][40]. The secondary and tertiary structures are preserved during the simulation, although the beta sheets regions are more flexible in the alpha helical regions.…”

Section: Description Of the Protein Dynamicsmentioning

confidence: 99%

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Computation of the mean residence time of water in the hydration shells of biomolecules

1993

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An algorithm is presented within the context of the calculation of the time-relaxation behavior of the hydration shells around atomic sites in biomolecules. We report a calculation of the time-relaxation behavior of the first and second hydration shells of polar, hydrophobic, and charged groups in a protein, crambin. The water mean residence times around protein groups are obtained from averages over configurations sampled during a 325-ps molecular dynamics simulation of crambin in solution. A convolution arising in the calculation of the mean relaxation time is implemented using a parallel prefix operator. A new characterization is given of the parallel prefii operator as a linear transformation, and this formulation enables us to derive efficient factorization of the convolution as a product of two parallel prefix operations. The parallel prefix operations are implemented in logarithmic time.

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Section: Description Of the Protein Dynamicsmentioning

confidence: 99%

“…The mean residence time of water molecules around Notice that most of the fluctuations occur for residues 1 and 33-39. These residues belong to beta sheet regions (residues 1-4 and 32-35) and coil regions (residues [36][37][38][39][40].…”

Section: Description Of Water Mean Residence Time Around Crambin Sidementioning

confidence: 99%

Computation of the mean residence time of water in the hydration shells of biomolecules

1993

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“…Solid state NMR experiments show that water deuterium atoms in crystals of lysozyme (26), ribonuclease (26), and crambin (27) undergo a mobile to stationary transition at Ϸ180 K. Water dynamics in crambin crystals match these enzymes. Further, the hydrophobic͞hydrophilic accessible surface area in crambin crystals is very close to that found in carboxypeptidase and myoglobin crystals (28).…”

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confidence: 97%

On the nature of a glassy state of matter in a hydrated protein: Relation to protein function

Teeter

Yamano

Stec

et al. 2001

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

122

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“…Protein hydration water was shown to be only slightly less dynamic and 10-15% denser than bulk water due to defects in the H-bond network induced by the protein surface (21,22). Interestingly, the hydration shell of soluble proteins does not freeze below the freezing temperature of the bulk solution (23,24). For frozen ubiquitin solutions, Tompa and coworkers showed that the hydration layer starts to freeze at about −50°C (25).…”

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confidence: 99%

Protein–ice interaction of an antifreeze protein observed with solid-state NMR

Siemer

Huang

McDermott

2010

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

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NMR on frozen solutions is an ideal method to study fundamental questions of macromolecular hydration, because the hydration shell of many biomolecules does not freeze together with bulk solvent. In the present study, we present previously undescribed NMR methods to study the interactions of proteins with their hydration shell and the ice lattice in frozen solution. We applied these methods to compare solvent interaction of an ice-binding type III antifreeze protein (AFP III) and ubiquitin a non-ice-binding protein in frozen solution. We measured 1 H-1 H cross-saturation and cross-relaxation to provide evidence for a molecular contact surface between ice and AFP III at moderate freezing temperatures of −35°C. This phenomenon is potentially unique for AFPs because ubiquitin shows no such cross relaxation or cross saturation with ice. On the other hand, we detected liquid hydration water and strong water-AFP III and water-ubiquitin cross peaks in frozen solution using relaxation filtered 2 H and HETCOR spectra with additional 1 H-1 H mixing. These results are consistent with the idea that ubiquitin is surrounded by a hydration shell, which separates it from the bulk ice. For AFP III, the water cross peaks indicate that only a portion of its hydration shell (i.e., at the ice-binding surface) is in contact with the ice lattice. The rest of AFP III's hydration shell behaves similarly to the hydration shell of non-ice-interacting proteins such as ubiquitin and does not freeze together with the bulk water.hydration shell | type III AFP | ice binding | water solute interaction A ntifreeze proteins (AFPs) can be found in a variety of coldadapted organisms including bacteria, plants, insects, and fish (1). AFPs lower the freezing point of a given solution below its melting point, a process called thermal hysteresis. This thermal hysteresis is thought to result from the strong binding of the AFP to the surface of ice crystals making their further growth energetically unfavorable (2, 3). One of the most intensely studied classes of AFPs is the type III AFPs from the ocean pound. In particular the HPLC-12 isoform (in the following just termed AFP III), was studied with X-ray crystallography (4), NMR (5, 6), mutagenesis (4,7,8), and molecular dynamics (9). These studies showed that the ice-binding site of AFP III is a flat surface formed by predominantly nonpolar residues (5, 8), which is remarkable because the solvent accessible surface of other soluble proteins like ubiquitin are predominantly polar. There have been limited opportunities to study the water molecules at the ice-binding surface of AFPs, although recent computational and sub-angstrom X-ray structures indicate ordered water molecules at the ice-binding surface (9, 10).Ice, with its very slow 1 H spin-lattice relaxation rate (R 1 ) and very fast spin-spin relaxation rate (R 2 ), is relatively difficult to study with NMR. Measurements of relaxation rates of ice showed that R 2 is on the order of 10 6 s −1 and R 1 on the order of 10at a temperatures of about 260 K...

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Orientational ordering and dynamics of the hydrate and exchangeable hydrogen atoms in crystalline crambin

Cited by 49 publications

References 28 publications

Computation of the mean residence time of water in the hydration shells of biomolecules

Computation of the mean residence time of water in the hydration shells of biomolecules

On the nature of a glassy state of matter in a hydrated protein: Relation to protein function

Protein–ice interaction of an antifreeze protein observed with solid-state NMR

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