DirectContacts2: A network of direct physical protein interactions derived from high-throughput mass spectrometry experiments.

Cellular function is driven by the activity proteins in stable complexes. Protein complex assembly depends on the direct physical association of component proteins. Advances in macromolecular structure prediction with tools like AlphaFold and RoseTTAFold have greatly improved our ability to model these interactions , but an all-by-all analysis of the human proteome's ~200M possible pairs remains computationally intractable.

Evaluation of the NHS England Low-Calorie Diet implementation pilot: a coproduced mixed-method study.

Background: National Health Service England piloted a low-calorie diet programme, delivered through total diet replacement and behaviour change support via 1 : 1, group or digital delivery, to improve type 2 diabetes in adults with excess weight.

Aim: To coproduce a qualitative and economic evaluation of the National Health Service low-calorie diet pilot, integrated with National Health Service data to provide an enhanced understanding of the long-term cost-effectiveness, implementation, equity and transferability across broad and diverse populations.

Research Questions: What are the theoretical principles, behaviour change components, content and mode of delivery of the programme, and is it delivered with fidelity to National Health Service specifications? What are the service provider, user and National Health Service staff experiences of the programme? Do sociodemographics influence programme access, uptake, compliance and success? What aspects of the service work and what do not work, for whom, in what context and why? Can the programme be improved to enhance patient experience and address inequities? What are the programme delivery costs, and policy implications for wide-spread adoption?

Methods: A mixed-methods study underpinned by a realist-informed approach was delivered across five work packages, involving: semistructured interviews with service users ( = 67), National Health Service staff ( = 55), service providers ( = 9); 13 service provider focus groups; and service user surveys ( = 719).

The human ciliopathy protein RSG1 links the CPLANE complex to transition zone architecture.

Cilia are essential organelles, and variants in genes governing ciliary function result in ciliopathic diseases. The Ciliogenesis and PLANar polarity Effectors (CPLANE) protein complex is essential for ciliogenesis, and all but one subunit of the CPLANE complex have been implicated in human ciliopathy. Here, we identify three families in which variants in the remaining CPLANE subunit CPLANE2/RSG1 also cause ciliopathy.

hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments.

Macromolecular protein complexes carry out most cellular functions. Unfortunately, we lack the subunit composition for many human protein complexes. To address this gap we integrated >25,000 mass spectrometry experiments using a machine learning approach to identify >15,000 human protein complexes.

Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes.

The Complex Portal (www.ebi.ac.

hu.MAP3.0: Atlas of human protein complexes by integration of > 25,000 proteomic experiments.

Macromolecular protein complexes carry out most functions in the cell including essential functions required for cell survival. Unfortunately, we lack the subunit composition for all human protein complexes. To address this gap we integrated >25,000 mass spectrometry experiments using a machine learning approach to identify > 15,000 human protein complexes.

Identifying Ciliary Proteins in Mammalian Retinas using a Gentle Extraction Method.

Mutations in retinal primary cilia are responsible for human blindness but the mechanisms are not fully understood (Wheway et al., 2014). Characterizing the proteome of an organelle such as cilia, is a fruitful way to understand its function but methods often require considerable sample quantities.

Transferability of the NHS low-calorie diet programme: A qualitative exploration of factors influencing the programme's transfer ahead of wide-scale adoption.

Introduction: Although behavioural interventions have been found to help control type 2 diabetes (T2D), it is important to understand how the delivery context can influence implementation and outcomes. The NHS committed to testing a low-calorie diet (LCD) programme designed to support people living with excess weight and T2D to lose weight and improve diabetes outcomes. Understanding what influenced implementation during the programme pilot is important in optimising rollout.

A Qualitative evaluation in community settings in England exploring the experiences of coaches delivering the NHS Low Calorie Diet programme pilot to ethnically diverse participants.

Background: The management of type 2 diabetes (T2D) within diverse ethnic populations requires a culturally tailored approach. However, little is known about the experiences of coaches delivering interventions for T2D, such as the National Health Service (NHS) Low Calorie Diet (LCD) programme, to people from diverse ethnic backgrounds.

Objective: To explore the experiences of coaches delivering an NHS programme using total diet replacement approaches to individuals from diverse ethnic backgrounds, to inform the effective tailoring and equitable delivery of future interventions.

Is the NHS low-calorie diet programme delivered as planned? An observational study examining adherence of intervention delivery to service specification.

Obesity and Type 2 Diabetes Mellitus (T2DM) are chronic conditions with significant personal, societal, and economic impacts. Expanding on existing trial evidence, the NHS piloted a 52-week low-calorie diet programme for T2DM, delivered by private providers using total diet replacement products and behaviour change support. This study aimed to determine the extent to which providers and coaches adhered to the service specification outlined by NHS England.

Views, perceptions, and experiences of type 2 diabetes or weight management programs among minoritized ethnic groups living in high-income countries: A systematic review of qualitative evidence.

Background: Prevalence of both obesity and type 2 diabetes can be higher in patients from certain ethnic groups, yet uptake and adherence to current support within these groups is lower, leading to widening health inequalities in high-income countries.

Objectives: The main objective of this study is to understand the views, perceptions, and experiences of and barriers and facilitators in relation to the uptake and adherence to weight management and type 2 diabetes programs in minoritized ethnic groups in high-income countries.

Methods: CINAHL, MEDLINE, PsycINFO, Scopus, Academic Search Complete, and PubMed were searched for English language studies undertaken in community-dwelling adults residing in high-income countries, who are from a minoritized ethnic group within the country of study.

Normalisation and equity of referral to the NHS Low Calorie Diet programme pilot; a qualitative evaluation of the experiences of health care staff.

Background: Health and wellbeing can be profoundly impacted by both obesity and type 2 diabetes, while the normalisation and equity of care for people living with these non-communicable diseases remain as challenges for local health systems. The National Health Service Low Calorie Diet programme in England, aims to support people to achieve type 2 diabetes remission, while also reducing health inequalities. We have explored the experiences of health care staff who have made a referral to the LCD programme, while identifying effective and equitable delivery of programme referrals, and their normalisation into routine care.

South Asian individuals' experiences on the NHS low-calorie diet programme: a qualitative study in community settings in England.

Background: Existing literature examines barriers to the provision of ethnically diverse dietary advice, however, is not specific to total diet replacement (TDR). There is a lack of literature from the UK, limiting the potential applicability of existing findings and themes to the UK context. This study addresses this gap in research by interviewing participants of South Asian ethnicity who have undertaken the National Health Service (NHS) low-calorie diet programme (LCD) for people with type 2 diabetes living with overweight or obesity.

Come for the atmosphere, stay for the interactions: Deciphering small molecule partitioning into biomolecular condensates.

Optimizing pharmacokinetic properties remains challenging but is generally guided by a set of structural rules. However, no such rule set exists for intracellular distribution. Kilgore et al.

Can the delivery of behavioural support be improved in the NHS England Low-Calorie Diet Programme? An observational study of behaviour change techniques.

Background: Previous research has illustrated a drift in the fidelity of behaviour change techniques (BCTs) during the design of the pilot NHS England Low-Calorie Diet (NHS-LCD) Programme. This study evaluated a subsequent domain of fidelity, intervention delivery. Two research questions were addressed: (1) To what extent were BCTs delivered with fidelity to providers programme plans? (2) What were the observed barriers and facilitators to delivery?

Methods: A mixed-methods sequential explanatory design was employed.

Scaffold Matcher: A CMA-ES based algorithm for identifying hotspot aligned peptidomimetic scaffolds.

The design of protein interaction inhibitors is a promising approach to address aberrant protein interactions that cause disease. One strategy in designing inhibitors is to use peptidomimetic scaffolds that mimic the natural interaction interface. A central challenge in using peptidomimetics as protein interaction inhibitors, however, is determining how best the molecular scaffold aligns to the residues of the interface it is attempting to mimic.

The protein organization of a red blood cell.

Red blood cells (RBCs) (erythrocytes) are the simplest primary human cells, lacking nuclei and major organelles and instead employing about a thousand proteins to dynamically control cellular function and morphology in response to physiological cues. In this study, we define a canonical RBC proteome and interactome using quantitative mass spectrometry and machine learning. Our data reveal an RBC interactome dominated by protein homeostasis, redox biology, cytoskeletal dynamics, and carbon metabolism.

hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies.

A general principle of biology is the self-assembly of proteins into functional complexes. Characterizing their composition is, therefore, required for our understanding of cellular functions. Unfortunately, we lack knowledge of the comprehensive set of identities of protein complexes in human cells.

Co-fractionation/mass spectrometry to identify protein complexes.

Co-fractionation/mass spectrometry (CF/MS) is a flexible and powerful method to detect physical associations of proteins. CF/MS can be applied to any tissue or organism without the need for protein-specific antibodies or epitope tags. Here, we outline two alternate protocols for MS preparation of samples (containing low or high salt) and a computational pipeline (cfmsflow) that together allow the successful application of this approach.

Systematic Identification of Protein Phosphorylation-Mediated Interactions.

Protein phosphorylation is a key regulatory mechanism involved in nearly every eukaryotic cellular process. Increasingly sensitive mass spectrometry approaches have identified hundreds of thousands of phosphorylation sites, but the functions of a vast majority of these sites remain unknown, with fewer than 5% of sites currently assigned a function. To increase our understanding of functional protein phosphorylation we developed an approach (phospho-DIFFRAC) for identifying the phosphorylation-dependence of protein assemblies in a systematic manner.

Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins.

Ciliary motility is driven by axonemal dyneins that are assembled in the cytoplasm before deployment to cilia. Motile ciliopathy can result from defects in the dyneins themselves or from defects in factors required for their cytoplasmic pre-assembly. Recent work demonstrates that axonemal dyneins, their specific assembly factors, and broadly-acting chaperones are concentrated in liquid-like organelles in the cytoplasm called DynAPs (Dynein Axonemal Particles).

A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery.

Cell-type specific RNA-associated proteins are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RNA-associated proteins, we currently have few comprehensive rosters of cell-type specific RNA-associated proteins in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-associated proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.

A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies.

Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants.