Intricate temperature-induced phase transitions for amino acid quasi-racemates

Görbitz, Carl Henrik; Karen, Pavel; Andersen, Niels Lyhne

doi:10.1107/s0108767313095780

Cited by 4 publications

(1 citation statement)

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“…Recently we have shown that this behaviour is not limited to regular racemates, but also pertain to quasi-racemates, including l-Nva:d-Met, l-Nva:d-Nle and l-Nle:d-Met. [162] Furthermore, enantiomeric amino acids with linear side chains also have interesting phase behaviour. Met has one room temperature and two high-temperature phases where the space group remains P2 1 , but with small changes to cell parameters and side-chain disorder.…”

Section: Temperature-induced Phase Transitionsmentioning

confidence: 99%

Crystal structures of amino acids: from bond lengths in glycine to metal complexes and high-pressure polymorphs

Görbitz

2015

Crystallography Reviews

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After the discovery of X-ray diffraction by crystals, amino acids were among the first organic compounds to have their solid-state structures investigated. The Cambridge Structural Database now contains more than 3500 entries for α-amino acids alone. After a short introduction dealing with the early history of X-ray structure determination, this review provides a classification of amino acid structures, describes essential structural elements, especially hydrogen bonding preferences and coordination to metal ions, and considers recent investigations on phase transitions as the result of extreme temperatures or pressure.

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Section: Temperature-induced Phase Transitionsmentioning

confidence: 99%

Crystal structures of amino acids: from bond lengths in glycine to metal complexes and high-pressure polymorphs

Görbitz

2015

Crystallography Reviews

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Dissection of the Water Cavity of Yeast Thioredoxin 1: The Effect of a Hydrophobic Residue in the Cavity

Iqbal

Gomes-Neto

Myiamoto³

et al. 2015

Biochemistry

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The water cavity of yeast thioredoxin 1 (yTrx1) is an ancestral, conserved structural element that is poorly understood. We recently demonstrated that the water cavity is involved in the complex protein dynamics that are responsible for the catalytically relevant event of coupling hydration, proton exchange, and motion at the interacting loops. Its main feature is the presence of the conserved polar residue, Asp24, which is buried in a hydrophobic cavity. Here, we evaluated the role of the solvation of Asp24 as the main element that is responsible for the formation of the water cavity in thioredoxins. We showed that the substitution of Asp24 with a hydrophobic residue (D24A) was not sufficient to completely close the cavity. The dynamics of the D24A mutant of yTrx1 at multiple time scales revealed that the D24A mutant presents motions at different time scales near the active site, interaction loops, and water cavity, revealing the existence of a smaller dissected cavity. Molecular dynamics simulation, along with experimental molecular dynamics, allowed a detailed description of the water cavity in wild-type yTrx1 and D24A. The cavity connects the interacting loops, the central β-sheet, and α-helices 2 and 4. It is formed by three contiguous lobes, which we call lobes A-C. Lobe A is hydrophilic and the most superficial. It is formed primarily by the conserved Lys54. Lobe B is the central lobe formed by the catalytically important residues Cys33 and Asp24, which are strategically positioned. Lobe C is the most hydrophobic and is formed by the conserved cis-Pro73. The central lobe B is closed upon introduction of the D24A mutation, revealing that independent forces other than solvation of Asp24 maintain lobes A and C in the open configuration. These data allow us to better understand the properties of this enzyme.

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Hydration and Conformational Equilibrium in Yeast Thioredoxin 1: Implication for H⁺ Exchange

et al. 2014

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One of the ancestral features of thioredoxins is the presence of a water cavity. Here, we report that a largely hydrated, conserved, buried aspartic acid in the water cavity modulates the dynamics of the interacting loops of yeast thioredoxin 1 (yTrx1). It is well-established that the aspartic acid, Asp24 for yTrx1, works as a proton acceptor in the reduction of the target protein. We propose a complementary role for Asp24 of coupling hydration and conformational motion of the water cavity and interacting loops. The intimate contact between the water cavity and the interacting loops means that motion at the water cavity will affect the interacting loops and vice versa. The D24N mutation alters the conformational equilibrium for both the oxidized and reduced states, quenching the conformational motion in the water cavity. By measuring the hydration and molecular dynamics simulation of wild-type yTrx1 and the D24N mutant, we showed that Asn24 is more exposed to water than Asp24 and the water cavity is smaller in the mutant, closing the inner part of the water cavity. We discuss how the conformational equilibrium contributes to the mechanism of catalysis and H(+) exchange.

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Intricate temperature-induced phase transitions for amino acid quasi-racemates

Cited by 4 publications

References 4 publications

Crystal structures of amino acids: from bond lengths in glycine to metal complexes and high-pressure polymorphs

Crystal structures of amino acids: from bond lengths in glycine to metal complexes and high-pressure polymorphs

Dissection of the Water Cavity of Yeast Thioredoxin 1: The Effect of a Hydrophobic Residue in the Cavity

Hydration and Conformational Equilibrium in Yeast Thioredoxin 1: Implication for H⁺ Exchange

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Intricate temperature-induced phase transitions for amino acid quasi-racemates

Cited by 4 publications

References 4 publications

Crystal structures of amino acids: from bond lengths in glycine to metal complexes and high-pressure polymorphs

Crystal structures of amino acids: from bond lengths in glycine to metal complexes and high-pressure polymorphs

Dissection of the Water Cavity of Yeast Thioredoxin 1: The Effect of a Hydrophobic Residue in the Cavity

Hydration and Conformational Equilibrium in Yeast Thioredoxin 1: Implication for H+ Exchange

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Hydration and Conformational Equilibrium in Yeast Thioredoxin 1: Implication for H⁺ Exchange