BraggNet: integrating Bragg peaks using neural networks

et al. 2021

Nat Commun

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Human manganese superoxide dismutase is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers are used by the enzyme to rid the mitochondria of O2•−. The mechanisms of concerted transfer enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules at particular redox states. Here, neutron diffraction of two redox-controlled manganese superoxide dismutase crystals reveal the all-atom structures of Mn3+ and Mn2+ enzyme forms. The structures deliver direct data on protonation changes between oxidation states of the metal. Observations include glutamine deprotonation, the involvement of tyrosine and histidine with altered pKas, and four unusual strong-short hydrogen bonds, including a low barrier hydrogen bond. We report a concerted proton and electron transfer mechanism for human manganese superoxide dismutase from the direct visualization of active site protons in Mn3+ and Mn2+ redox states.

Section: Methodsmentioning

confidence: 99%

Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase

Azadmanesh¹,

Lutz²,

et al. 2021

Nat Commun

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“…Data collection was completed in 7.5 days, yielding a dataset of good completeness to a resolution of 1.50 Å (Table 1 ). These data were reduced with the Mantid program ( 39 ) using newly developed 3D profile fitting for time-of-flight diffraction data ( 40 , 41 ). Integrated intensities were then scaled using Lauenorm from the Lauegen suite ( 42 , 43 ).…”

Section: Methodsmentioning

confidence: 99%

Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography

Harp

Sullivan

et al. 2021

Nucleic Acids Research

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Even in high-quality X-ray crystal structures of oligonucleotides determined at a resolution of 1 Å or higher, the orientations of first-shell water molecules remain unclear. We used cryo neutron crystallography to gain insight into the H-bonding patterns of water molecules around the left-handed Z-DNA duplex [d(CGCGCG)]2. The neutron density visualized at 1.5 Å resolution for the first time allows us to pinpoint the orientations of most of the water molecules directly contacting the DNA and of many second-shell waters. In particular, H-bond acceptor and donor patterns for water participating in prominent hydration motifs inside the minor groove, on the convex surface or bridging nucleobase and phosphate oxygen atoms are finally revealed. Several water molecules display entirely unexpected orientations. For example, a water molecule located at H-bonding distance from O6 keto oxygen atoms of two adjacent guanines directs both its deuterium atoms away from the keto groups. Exocyclic amino groups of guanine (N2) and cytosine (N4) unexpectedly stabilize waters H-bonded to O2 keto oxygens from adjacent cytosines and O6 keto oxygens from adjacent guanines, respectively. Our structure offers the most detailed view to date of DNA solvation in the solid-state undistorted by metal ions or polyamines.

“…Data processing and refinement. Neutron data were integrated using MANTID 60 . Integrated neutron data were scaled and wavelength-normalized using LAUENORM from the LAUGEN suite 61 .…”

Section: Methodsmentioning

confidence: 99%

Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase

Azadmanesh

Lutz

et al. 2020

Preprint

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Human manganese superoxide dismutase (MnSOD) is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers (CPETs) are used by the enzyme to rid the mitochondria of superoxide, a precursor to other harmful reactive oxygen and nitrogen species. The mechanisms of CPET-utilizing enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules involved in catalysis while controlling the redox state of the enzyme. Here, neutron diffraction of redox-controlled MnSOD crystals revealed the all-atom structures of Mn3+SOD and Mn2+SOD delivering unique data on sites of differential protonation. A novel mechanism is proposed from the direct observation of glutamine deprotonation, the involvement of Tyr and His with altered pKas, and three unusual strong-short hydrogen bonds that change with the oxidation state of the metal. Quantum calculations provide insight into the electronic modulation of the observed structures.