Mikkelsen, Maria Dalgaard Tran, Vy Ha Nguyen Meier, Sebastian Nguyen, Thuan Thi Holck, Jesper Cao, Hang Thi Thuy Van, Tran Thi Thanh Thinh, Pham Duc Meyer, Anne S Morth, Jens Preben
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Published in
Acta crystallographica. Section D, Structural biology
Fucoidanases (EC 3.2.1.-) catalyze the hydrolysis of glycosidic bonds between fucose residues in fucoidans. Fucoidans are a compositionally and structurally diverse class of fucose-containing sulfated polysaccharides that are primarily found in brown seaweeds. Here, the structural characterization of a novel endo-α(1,4)-fucoidanase, Mef1, from the ...
Negron Teron, Kristos I Das, Chittaranjan
Published in
Acta crystallographica. Section D, Structural biology
Structural characterization of the recognition of ubiquitin (Ub) by deubiquitinases (DUBs) has largely relied on covalent complexation of the DUB through its catalytic cysteine with a Ub C-terminal electrophile. The Ub electrophiles are accessed through intein chemistry in conjunction with chemical synthesis. Here, it was asked whether DUB-Ub coval...
Hicks, Alan Abraham, Paul Leite, Wellington Zhang, Qiu Weiss, Kevin L O'Neill, Hugh Petridis, Loukas Smith, Jeremy C
Published in
Acta crystallographica. Section D, Structural biology
The contrast-variation method in small-angle neutron scattering (SANS) is a uniquely powerful technique for determining the structure of individual components in biomolecular systems containing regions of different neutron scattering length density ρ. By altering the ρ of the target solute and the solvent through judicious incorporation of deuteriu...
Kascakova, Barbora Kotal, Jan Havlickova, Petra Vopatkova, Vera Prudnikova, Tatyana Grinkevich, Pavel Kuty, Michal Chmelar, Jindrich Kuta Smatanova, Ivana
Published in
Acta crystallographica. Section D, Structural biology
Iripin-4, one of the many salivary serpins from Ixodes ricinus ticks with an as-yet unexplained function, crystallized in two different structural conformations, namely the native partially relaxed state and the cleaved serpin. The native structure was solved at a resolution of 2.3 Å and the structure of the cleaved conformation was solved at 2.0 Å...
Wych, David C Aoto, Phillip C Vu, Lily Wolff, Alexander M Mobley, David L Fraser, James S Taylor, Susan S Wall, Michael E
Published in
Acta crystallographica. Section D, Structural biology
It is investigated whether molecular-dynamics (MD) simulations can be used to enhance macromolecular crystallography (MX) studies. Historically, protein crystal structures have been described using a single set of atomic coordinates. Because conformational variation is important for protein function, researchers now often build models that contain ...
Trewhella, Jill Vachette, Patrice Bierma, Jan Blanchet, Clement Brookes, Emre Chakravarthy, Srinivas Chatzimagas, Leonie Cleveland, Thomas E 4th Cowieson, Nathan Crossett, Ben
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Published in
Acta crystallographica. Section D, Structural biology
Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtrac...
Yabukarski, Filip Doukov, Tzanko Mokhtari, Daniel A Du, Siyuan Herschlag, Daniel
Published in
Acta crystallographica. Section D, Structural biology
Cryo-cooling has been nearly universally adopted to mitigate X-ray damage and facilitate crystal handling in protein X-ray crystallography. However, cryo X-ray crystallographic data provide an incomplete window into the ensemble of conformations that is at the heart of protein function and energetics. Room-temperature (RT) X-ray crystallography pro...
Babnigg, Gyorgy Sherrell, Darren Kim, Youngchang Johnson, Jessica L Nocek, Boguslaw Tan, Kemin Axford, Danny Li, Hui Bigelow, Lance Welk, Lukas
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Published in
Acta crystallographica. Section D, Structural biology
Protein crystals grown in microfluidic droplets have been shown to be an effective and robust platform for storage, transport and serial crystallography data collection with a minimal impact on diffraction quality. Single macromolecular microcrystals grown in nanolitre-sized droplets allow the very efficient use of protein samples and can produce l...
Chooback, Lilian Thomas, Leonard N Blythe, Nathan Karsten, William
Published in
Acta crystallographica. Section D, Structural biology
Dihydrodipicolinate synthase (DHDPS) catalyzes the first committed step in the lysine-biosynthetic pathway converting pyruvate and L-aspartate-β-semialdehyde to dihydrodipicolinate. Kinetic studies indicate that the pyruvate analog (S)-2-bromopropionate inactivates the enzyme in a pseudo-first-order process. An initial velocity pattern indicates th...
Dong, Jiahui Li, Daoyi Ozcan, Kadir Wan, Dayu Jiang, Wen Chen, Yingjie
Published in
Acta crystallographica. Section D, Structural biology
Cryogenic electron microscopy (cryoEM) has emerged as a revolutionary method for solving high-resolution structures and studying the dynamics of macromolecular complexes and viruses in near-native states. However, the availability of the equipment, and the time and cost needed for training, severely limit the opportunities for training. To solve th...
