Reliable structural interpretation of small-angle scattering data from bio-molecules in solution - The importance of quality control and a standard reporting framework

Small-angle scattering is becoming an increasingly popular tool for the study of bio-molecular structures in solution. The large number of publications with 3D-structural models generated from small-angle solution scattering data has led to a growing consensus for the need to establish a standard reporting framework for their publication. The International Union of Crystallography recently established a set of guidelines for the necessary information required for the publication of such structural models. Here we describe the rationale for these guidelines and the importance of standardising the way in which small-angle scattering data from bio-molecules and associated structural interpretations are reported. © 2012 Jacques et al.; licensee BioMed Central Ltd

Structure of the T109S mutant of Escherichia coli dihydroorotase complexed with the inhibitor 5-­fluoroorotate: catalytic activity is reflected by the crystal form

A single-point mutant (T109S) of E. coli dihydroorotase initially crystallizes so that the two monomers of the dimer are related by a crystallographic twofold axis. In the presence of substrate, conversion to the previously observed asymmetric dimer with substrate bound in one subunit and product in the other is observed

Challenging the ‘Good Fit’ Narrative: Creating Inclusive Recruitment Practices in Academic Libraries

Academic libraries operate under the assumption that there is one “right candidate” for a multi-layered position and that a search committee, a group of individuals formed with the purpose of assisting a responsible administrator in the recruiting and screening of candidates for a posted academic position, is the fairest and most equitable approach to hiring academic librarians. That assumption is running up against the fact that libraries and academic libraries in particular have an acknowledged a problem with recruiting and retaining librarians of color. According to the latest edition of the American Library Association Diversity Counts report, librarianship remains an overwhelmingly white profession: approximately 88% of credentialed academic librarians are white. There are countless articles bemoaning the state of racial diversity in librarianship and multiple research studies have made recommendations for creating a better culture for diversity, assessing diversity initiatives in librarianship, and retaining librarians of color. However there are no empirical research studies in library literature that have examined the ways in which libraries hire and recruit librarians for diversity. In fact much of the literature perpetuates the idea of hiring a candidate who is a “good cultural fit,” which ultimately is a practice of reproducing the status quo. This paper examines the ways in which hiring practices in academic libraries perpetuate whiteness and undermine libraries’ attempts to recruit for diversity

Challenging the ‘Good Fit’ Narrative: Creating Inclusive Recruitment Practices in Academic Libraries

Academic libraries operate under the assumption that there is one “right candidate” for a multi-layered position and that a search committee, a group of individuals formed with the purpose of assisting a responsible administrator in the recruiting and screening of candidates for a posted academic position, is the fairest and most equitable approach to hiring academic librarians. That assumption is running up against the fact that libraries and academic libraries in particular have an acknowledged a problem with recruiting and retaining librarians of color. According to the latest edition of the American Library Association Diversity Counts report, librarianship remains an overwhelmingly white profession: approximately 88% of credentialed academic librarians are white. There are countless articles bemoaning the state of racial diversity in librarianship and multiple research studies have made recommendations for creating a better culture for diversity, assessing diversity initiatives in librarianship, and retaining librarians of color. However there are no empirical research studies in library literature that have examined the ways in which libraries hire and recruit librarians for diversity. In fact much of the literature perpetuates the idea of hiring a candidate who is a “good cultural fit,” which ultimately is a practice of reproducing the status quo. This paper examines the ways in which hiring practices in academic libraries perpetuate whiteness and undermine libraries’ attempts to recruit for diversity

Challenging the ‘Good Fit’ Narrative: Creating Inclusive Recruitment Practices in Academic Libraries

Academic libraries operate under the assumption that there is one “right candidate” for a multi-layered position and that a search committee, a group of individuals formed with the purpose of assisting a responsible administrator in the recruiting and screening of candidates for a posted academic position, is the fairest and most equitable approach to hiring academic librarians. That assumption is running up against the fact that libraries and academic libraries in particular have an acknowledged a problem with recruiting and retaining librarians of color. According to the latest edition of the American Library Association Diversity Counts report, librarianship remains an overwhelmingly white profession: approximately 88% of credentialed academic librarians are white. There are countless articles bemoaning the state of racial diversity in librarianship and multiple research studies have made recommendations for creating a better culture for diversity, assessing diversity initiatives in librarianship, and retaining librarians of color. However there are no empirical research studies in library literature that have examined the ways in which libraries hire and recruit librarians for diversity. In fact much of the literature perpetuates the idea of hiring a candidate who is a “good cultural fit,” which ultimately is a practice of reproducing the status quo. This paper examines the ways in which hiring practices in academic libraries perpetuate whiteness and undermine libraries’ attempts to recruit for diversity

Crystal structure of the ϵ subunit of the proton-translocating ATP synthase from Escherichia coli

AbstractBackground: Proton-translocating ATP synthases convert the energy generated from photosynthesis or respiration into ATP. These enzymes, termed F0F1-ATPases, are structurally highly conserved. In Escherichia coli, F0F1-ATPase consists of a membrane portion, F0, made up of three different polypeptides (a, b and c) and an F1 portion comprising five different polypeptides in the stoichiometry α3β3γδϵ. The minor subunits γ, δ and ϵ are required for the coupling of proton translocation with ATP synthesis; the ϵ subunit is in close contact with the α, β , γ and c subunits. The structure of the ϵ subunit provides clues to its essential role in this complex enzyme.Results: The structure of the E. coli F0F1-ATPase ϵ subunit has been solved at 2.3 Å resolution by multiple isomorphous replacement. The structure, comprising residues 2–136 of the polypeptide chain and 14 water molecules, refined to an R value of 0.214 (Rfree = 0.288). The molecule has a novel fold with two domains. The N-terminal domain is a β sandwich with two five-stranded sheets. The C-terminal domain is formed from two α helices arranged in an antiparallel coiled-coil. A series of alanine residues from each helix form the central contacting residues in the helical domain and can be described as an ‘alanine zipper’. There is an extensive hydrophobic contact region between the two domains providing a stable interface. The individual domains of the crystal structure closely resemble the structures determined in solution by NMR spectroscopy.Conclusions: Sequence alignments of a number of ϵ subunits from diverse sources suggest that the C-terminal domain, which is absent in some species, is not essential for function. In the crystal the N-terminal domains of two ϵ subunits make a close hydrophobic interaction across a crystallographic twofold axis. This region has previously been proposed as the contact surface between the ϵ and γ subunits in the complete F1-ATPase complex. In the crystal structure, we observe what is apparently a stable interface between the two domains of the ϵ subunit, consistent with the fact that the crystal and solution structures are quite similar despite close crystal packing. This suggests that a gross conformational change in the ϵ subunit, to transmit the effect of proton translocation to the catalytic domain, is unlikely, but cannot be ruled out

Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution

Small-angle scattering is becoming a mainstream technique for structural molecular biology. As such, it is important to establish guidelines for publication that will ensure that there is adequate reporting of the data and its treatment so that reviewers and readers can independently assess the quality of the data and the basis for any interpretations presented. This article presents a set of preliminary guidelines that emerged after consultation with the IUCr Commission on Small-Angle Scattering and other experts in the field and discusses the rationale for their application. At the 2011 Congress of the IUCr in Madrid, the Commission on Journals agreed to adopt these preliminary guidelines for the presentation of biomolecular structures from small-angle scattering data in IUCr publications. Here, these guidelines are outlined and the reasons for standardizing the way in which small-angle scattering data are presented. © 2012 International Union of Crystallography Printed in Singapore - all rights reserved

The Initiation of GTP Hydrolysis by the G-Domain of FeoB: Insights from a Transition-State Complex Structure

The polytopic membrane protein FeoB is a ferrous iron transporter in prokaryotes. The protein contains a potassium-activated GTPase domain that is essential in regulating the import of iron and conferring virulence to many disease-causing bacteria. However, the mechanism by which the G-domain of FeoB hydrolyzes GTP is not well understood. In particular, it is not yet known how the pivotal step in GTP hydrolysis is achieved: alignment of a catalytic water molecule. In the current study, the crystal structure of the soluble domains from Streptococcus thermophilus FeoB (NFeoBSt) in complex with the activating potassium ion and a transition-state analogue, GDP⋅AlF4−, reveals a novel mode of water alignment involving contacts with the protein backbone only. In parallel to the structural studies, a series of seven mutant proteins were constructed that targeted conserved residues at the active site of NFeoBSt, and the nucleotide binding and hydrolysis properties of these were measured and compared to the wild-type protein. The results show that mutations in Thr35 abolish GTPase activity of the protein, while other conserved residues (Tyr58, Ser64, Glu66 and Glu67) are not required for water alignment by NFeoBSt. Together with the crystal structure, the findings suggest a new mechanism for hydrolysis initiation in small G-proteins, in which the attacking water molecule is aligned by contacts with the protein backbone only

Cognitive mediation in people with dementia:Development, structural, and construct validity of the first dementia‐specific measure

OBJECTIVES: Anxiety and depression are common and deleterious comorbidities in people living with dementia (PLWD). Cognitive behavioural therapy (CBT) is one of the few promising treatments; however, it is unclear whether PLWD have the necessary prerequisites to engage in this. Having an understanding of cognitive mediation, that a thought mediates the relationship between an antecedent event and its emotional consequence, is key for engaging with CBT and is also a critical component of emotion regulation. There are no measures of this construct validated for PLWD. This study aims to adapt and validate an existing measure for this population. A secondary aim is to assess its applicability in older adults (OA) without a recognised neurocognitive impairment. // METHODS: A measure of cognitive mediation was adapted via expert and service user consultation for use in PLWD. A total of 102 PLWD and 77 OA without neurocognitive impairments completed the adapted measure along with two measures of emotion recognition and reasoning. Factor structure was examined separately in both samples, and the measure reduced, with convergent validity assessed. // RESULTS: A final measure of 10 items (named the CM-Dem) was subject to factor analysis yielding a single factor solution. The measure showed good psychometric properties in PLWD, including good model fit, high internal consistency, inter-rater reliability, and moderate convergent validity with related constructs. In contrast, poor validity was found in OA, especially a lack of convergent validity. // CONCLUSIONS: The CM-Dem has clinical and research utility as a measure of cognitive mediation in PLWD, but less so in OA