[PDF][PDF] Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM

RA Nicholls, M Tykac, O Kovalevskiy… - … Section D: Structural …, 2018 - journals.iucr.org
Recent advances in instrumentation and software have resulted in cryo-EM rapidly
becoming the method of choice for structural biologists, especially for those studying the …

[PDF][PDF] Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

A Brown, F Long, RA Nicholls, J Toots… - … Section D: Biological …, 2015 - journals.iucr.org
The recent rapid development of single-particle electron cryo-microscopy (cryo-EM) now
allows structures to be solved by this method at resolutions close to 3 Å. Here, a number of …

[PDF][PDF] Conformation-independent structural comparison of macromolecules with ProSMART

RA Nicholls, M Fischer, S McNicholas… - … Section D: Biological …, 2014 - journals.iucr.org
The identification and exploration of (dis) similarities between macromolecular structures
can help to gain biological insight, for instance when visualizing or quantifying the response …

Crystallographic phasing from weak anomalous signals

Q Liu, WA Hendrickson - Current opinion in structural biology, 2015 - Elsevier
Highlights•Crystal handling to reduce damage, variations and background.•Beamline
instrumentation and data collection strategies for weak anomalous signals.•High multiplicity …

[PDF][PDF] Modelling covalent linkages in CCP4

RA Nicholls, RP Joosten, F Long, M Wojdyr… - … Section D: Structural …, 2021 - journals.iucr.org
In this contribution, the current protocols for modelling covalent linkages within the CCP4
suite are considered. The mechanism used for modelling covalent linkages is reviewed: the …

Structural basis for 2′-deoxyguanosine recognition by the 2′-dG-II class of riboswitches

MM Matyjasik, RT Batey - Nucleic Acids Research, 2019 - academic.oup.com
A recent bioinformatic analysis of well-characterized classes of riboswitches uncovered
subgroups unable to bind to the regulatory molecule of the parental class. Within the …

Conformation-dependent restraints for polynucleotides: I. Clustering of the geometry of the phosphodiester group

M Kowiel, D Brzezinski, M Jaskolski - Nucleic Acids Research, 2016 - academic.oup.com
The refinement of macromolecular structures is usually aided by prior stereochemical
knowledge in the form of geometrical restraints. Such restraints are also used for the flexible …

Toward development of epigenetic drugs for central nervous system disorders: Modulating neuroplasticity via H3K4 methylation

EL Ricq, JM Hooker, SJ Haggarty - Psychiatry and clinical …, 2016 - Wiley Online Library
The mammalian brain dynamically activates or silences gene programs in response to
environmental input and developmental cues. This neuroplasticity is controlled by signaling …

An 1, 4-α-glucosyltransferase defines a new maltodextrin catabolism scheme in Lactobacillus acidophilus

S Andersen, MS Møller, JCN Poulsen… - Applied and …, 2020 - Am Soc Microbiol
The maltooligosaccharide (MOS) utilization locus in Lactobacillus acidophilus NCFM, a
model for human small-intestine lactobacilli, encodes three glycoside hydrolases (GHs): a …

A Noncanonical Metal Center Drives the Activity of the Sediminispirochaeta smaragdinae Metallo-β-lactamase SPS-1

Z Cheng, J VanPelt, A Bergstrom, C Bethel, A Katko… - Biochemistry, 2018 - ACS Publications
In an effort to evaluate whether a recently reported putative metallo-β-lactamase (MβL)
contains a novel MβL active site, SPS-1 from Sediminispirochaeta smaragdinae was …