Visualizing the Bohr effect in hemoglobin: neutron structure of equine cyanomethemoglobin in the R state and comparison with human deoxyhemoglobin in the T state.
Acta Crystallogr D Struct Biol 72(Pt 7):892 (2016)
Neutron crystallography provides direct visual evidence of the atomic positions of deuterium-exchanged H atoms, enabling the accurate determination of the protonation/deuteration state of hydrated biomolecules. Comparison of two neutron structures of hemoglobins, human deoxyhemoglobin (T state) ...
Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.
Angewandte Chemie. International edition in Eng... 55(16):4924 (2016)
Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer i...
A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers.
Plant Physiology 170(1):123 (2016)
A cellulose synthesis complex with a "rosette" shape is responsible for synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembra...
Protein Kinase A Catalytic Subunit Primed for Action: Time-Lapse Crystallography of Michaelis Complex Formation.
Structure 23(12):2331 (2015)
The catalytic subunit of the cyclic AMP-dependent protein kinase A (PKAc) catalyzes the transfer of the γ-phosphate of bound Mg2ATP to a serine or threonine residue of a protein substrate. Here, time-lapse X-ray crystallography was used to capture a series of complexes of PKAc with an oligopepti...
Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.
PNAS 112(40):12384 (2015)
Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, ...
Phosphoryl Transfer Reaction Snapshots in Crystals: INSIGHTS INTO THE MECHANISM OF PROTEIN KINASE A CATALYTIC SUBUNIT.
Journal of Biological Chemistry 290(25):15538 (2015)
To study the catalytic mechanism of phosphorylation catalyzed by cAMP-dependent protein kinase (PKA) a structure of the enzyme-substrate complex representing the Michaelis complex is of specific interest as it can shed light on the structure of the transition state. However, all previous crystal...
Determination of cellulose crystallinity from powder diffraction diagrams.
Biopolymers 103(2):67 (2015)
One-dimensional (1D) (spherically averaged) powder diffraction diagrams are commonly used to determine the degree of cellulose crystallinity in biomass samples. Here, it is shown using molecular modeling how disorder in cellulose fibrils can lead to considerable uncertainty in conclusions drawn ...
MARTINI coarse-grained model for crystalline cellulose microfibers.
Journal of Physical Chemistry B 119(2):465 (2015)
Commercial-scale biofuel production requires a deep understanding of the structure and dynamics of its principal target: cellulose. However, an accurate description and modeling of this carbohydrate structure at the mesoscale remains elusive, particularly because of its overwhelming length scale...
Why genetic modification of lignin leads to low-recalcitrance biomass.
Physical Chemistry Chemical Physics 17(1):358 (2015)
Genetic modification of plants via down-regulation of cinnamyl alcohol dehydrogenase leads to incorporation of aldehyde groups in the lignin polymer. The resulting lignocellulosic biomass has increased bioethanol yield. However, a molecular-scale explanation of this finding is currently lacking....
Production of bacterial cellulose with controlled deuterium-hydrogen substitution for neutron scattering studies.
Methods in Enzymology 565:123 (2015)
Isotopic enrichment of biomacromolecules is a widely used technique that enables the investigation of the structural and dynamic properties to provide information not accessible with natural abundance isotopic composition. This study reports an approach for deuterium incorporation into bacterial...
Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography.
PNAS 111(51):18225 (2014)
Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate (DHF) to tetrahydrofolate (THF). An important step in the mechanism involves proton donation to the N5 atom of DHF. The inability to determine the protonation states of active site residues and substrate has ...
Hydration control of the mechanical and dynamical properties of cellulose.
Biomacromolecules 15(11):4152 (2014)
The mechanical and dynamical properties of cellulose, the most abundant biomolecule on earth, are essential for its function in plant cell walls and advanced biomaterials. Cellulose is almost always found in a hydrated state, and it is therefore important to understand how hydration influences i...
L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study.
Structure 22(9):1287 (2014)
D-xylose isomerase (XI) is capable of sugar isomerization and slow conversion of some monosaccharides into their C2-epimers. We present X-ray and neutron crystallographic studies to locate H and D atoms during the respective isomerization and epimerization of L-arabinose to L-ribulose and L-ribo...
Preliminary joint X-ray and neutron protein crystallographic studies of ecDHFR complexed with folate and NADP+.
Acta crystallographica. Section F, Structural b... 70(Pt 6):814 (2014)
A crystal of Escherichia coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP+ of 4×1.3×0.7 mm (3.6 mm3) in size was obtained by sequential application of microseeding and macroseeding. A neutron diffraction data set was collected to 2.0 Å resolution using the IMAGINE diffractome...
Metal-free cAMP-dependent protein kinase can catalyze phosphoryl transfer.
Biochemistry (Washington) 53(19):3179 (2014)
X-ray structures of several ternary product complexes of the catalytic subunit of cAMP-dependent protein kinase (PKAc) have been determined with no bound metal ions and with Na(+) or K(+) coordinated at two metal-binding sites. The metal-free PKAc and the enzyme with alkali metals were able to f...
Hydrolysis of DFP and the nerve agent (S)-sarin by DFPase proceeds along two different reaction pathways: implications for engineering bioscavengers.
Journal of Physical Chemistry B 118(17):4479 (2014)
Organophosphorus (OP) nerve agents such as (S)-sarin are among the most highly toxic compounds that have been synthesized. Engineering enzymes that catalyze the hydrolysis of nerve agents ("bioscavengers") is an emerging prophylactic approach to diminish their toxic effects. Although its native ...
Engineering acidic Streptomyces rubiginosus D-xylose isomerase by rational enzyme design.
Protein Engineering Design and Selection 27(2):59 (2014)
To maximize bioethanol production from lignocellulosic biomass, all sugars must be utilized. Yeast fermentation can be improved by introducing the d-xylose isomerase enzyme to convert the pentose sugar d-xylose, which cannot be fermented by Saccharomyces cerevisiae, into the fermentable ketose d...
X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism.
Acta Crystallographica Section D 70(Pt 1):11 (2014)
Xylanases catalyze the hydrolysis of plant hemicellulose xylan into oligosaccharides by cleaving the main-chain glycosidic linkages connecting xylose subunits. To study ligand binding and to understand how the pH constrains the activity of the enzyme, variants of the Trichoderma reesei xylanase ...
Effect of lignin content on changes occurring in poplar cellulose ultrastructure during dilute acid pretreatment.
Biotechnology for Biofuels 7(1):150 (2014)
Obtaining a better understanding of the complex mechanisms occurring during lignocellulosic deconstruction is critical to the continued growth of renewable biofuel production. A key step in bioethanol production is thermochemical pretreatment to reduce plant cell wall recalcitrance for downstrea...
Seeing the chemistry in biology with neutron crystallography.
Physical Chemistry Chemical Physics 15(33):13705 (2013)
New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible with neutrons. Using X-rays allows one to see structure, while neutrons al...