NIHRDataInsights/HRCSData huggingface dataset:
Title: Membrane protein folding: from simplistic models to the biological reality of co-translation
Funder: Wellcome Trust

Abstract: The folding of newly synthesised proteins to their correct structure is essential to attaining functionally normal proteins that are vital to health. I aim to transform understanding of membrane protein folding by advancing mechanistic studies to address the biosynthetic process of co-translational folding. Co-translational folding studies represent a new frontier. The majority of folding research studies artificially-denatured, full-length chains - a situation that is unrepresentative of cellular folding. Nearly all a helical membrane proteins fold co-translationally during biosynthesis, as the ribosome is translating mRNA. Thus the proteins fold in the membrane whilst the polypeptide chain is elongating, and not as full-length chains. I will develop kinetic approaches to trace the temporal evolution of structure of helical membrane proteins as their nascent chains are being synthesised by the ribosome. My focus will be bacterial inner membrane proteins and members of the ubiquitous Major Facilitator Superfamily of transporters. This proposal will addresses the following questions: 1. When does protein structure evolve during nascent chain elongation by the ribosome? 2. How is co-translational folding coupled to translation rate? 3. How is co-translational folding modulated by the lipid bilayer?

Lay abstract: Cells in our bodies communicate with the outside world via proteins embedded in membranes that surround cells. Like all components of living systems, membrane proteins must assemble themselves. This project will study how these vital membrane proteins get into shape. Genes carry the code for proteins, but how genetic information is translated into functional proteins remains unclear. Proteins begin as a string of amino acids, which then have to fold-up to the correct shape in the right part of the body. Flaws in folding result in malfunction and disease. I will study folding as it occurs in nature; namely whilst the protein amino acid string is being synthesised. Previous work has only looked at how proteins fold when fully formed and removed from their site of formation. As part of this step change in studying membrane protein folding, I will generate a high definition movie of the process.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Nuffield Council on Bioethics 2018 - 2022
Funder: Wellcome Trust

Abstract: This proposal seeks renewed support for the Nuffield Council on Bioethics, an independent bioethics advisory body that has been producing influential contributions to public and policy debates on ethical issues arising from developments in biological and medical research since 1991. Since 1993 its funding has been shared among the Medical Research Council, the Nuffield Foundation and the Wellcome Trust through a co-ordinated 5-year funding cycle. The Council’s terms of reference require it to: &bull;identify important ethical questions arising from recent developments in biological andmedical research; &bull;examine and report on those issues, engaging relevant stakeholders; &bull;inform and engage in policy and media debates; and &bull;make recommendations to policy-makers. The Council has, over 25 years, developed an international reputation for providing independent, critical ethical analysis of such new developments, and for preparing influential reports with advice to policy-makers. In doing so it has also succeeded in promoting wider public discussion of these issues, thus helping secure public confidence in the way science and medicine are developed. It has achieved a high profile in public, academic and national and international policy environments

Lay abstract: No Data Entered

Research activity codes: 8.3 POLICY, ETHICS AND RESEARCH GOVERNANCE
Health categories: GENERIC HEALTH RELEVANCE
Title: Scaling-up Health-Arts Programmes: Implementation and Effectiveness Research (SHAPER)
Funder: Wellcome Trust

Abstract: This proposed programme at King’s College London (King’s) and King’s Health Partners (KHP), and in close collaboration with University College London (UCL), will translate arts in health research into sustainable, standardised and scalable health interventions that make both clinical and economic sense. Our primary aim is to upscale three known effective arts interventions (Melodies for Mums for Postnatal Depression, Dance for Parkinson’s, and Stroke Odysseys) and embed them in a clinical pathway across KHP, thereby strengthening the case for NHS Clinical Commissioning Groups (CCGs) to recommend and fund such interventions in the long-term. We will seek to establish defined, clinical referral pathways, from either primary or secondary care settings. In addition, by examining larger cohorts than has hitherto been possible, we will gather further evidence of (i) the clinical effectiveness of our chosen interventions, and of the mechanisms underpinning it, (ii) the implementation effectiveness (i.e., acceptability, feasibility and appropriateness), and (iii) their economic effectiveness. The programme will further involve the largest implementation research centre outside North America, the King’s Centre for Implementation Science, as well as clinicians and researchers across King’s/KHP/UCL, and the three award-winning arts organisations, Breathe Arts Health Research, the English National Ballet and Rosetta Life.


Research activity codes: 8.1 ORGANISATION AND DELIVERY OF SERVICES
Health categories: GENERIC HEALTH RELEVANCE
Title: Defining the Haematopoietic System through Integrated Multi-Scale Analysis
Funder: Wellcome Trust

Abstract: Biological processes operate at vastly different scales ranging from molecules to entire organs. However, relating molecular insights to whole tissue function remains difficult since biomedical research commonly focusses on just a single scale. The Göttgens group has taken advantage of new single cell profiling technologies to generate a comprehensive landscape of the transcriptional states that a blood stem cell may traverse through when it differentiates into the various blood lineages. Here it is proposed to use this single cell transcriptional landscape to connect different scales ranging from molecular to cellular to whole tissue function, and thus advance our understanding of cell fate decision making in blood stem and progenitor cells. Complementary experimental and computational approaches will address how molecular regulatory networks control cellular identity, and how tissue-scale computer models of the blood system can be grounded in comprehensive molecular information. The proposed experiments are designed to provide new leads for subsequent studies, including potential new therapeutic targets from analysis of pre-leukaemic models. Moreover, empowering single cell transcriptional landscapes to link “molecular” observations with the function of the entire haematopoietic system will generate a framework that is broadly applicable to advance our understanding of all normal and pathological organ systems.

Lay abstract: The human body produces 3 million new blood cells every second to replace short-lived red and white blood cells. This constant process of blood formation critically depends on blood stem cells, which are long-lived and can divide to make all other types of blood cells. Tight regulation of blood cell formation is essential to prevent the development of fatal diseases such as leukaemia. This proposal takes advantage of recent technological innovations that allow analysis of regulatory processes in thousands of single cells. A combination of complementary experimental and computational methods will be employed to enhance our understanding of how blood stem cells decide whether or not they need to produce new white or red blood cells. It is also proposed to build a computer model that directly links the behaviour of the entire blood system with regulatory processes in individual cells, so that we can better predict for example the effectiveness of modern targeted drugs. This new framework will not only advance our understanding of normal blood stem cells and leukaemia, but also be broadly applicable to the study of other organs and diseases.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Understanding mammalian interphase genome structure in mouse ES cells
Funder: Wellcome Trust

Abstract: The folding of genomic DNA from the beads-on-a-string like structure of nucleosomes into higher order assemblies is critically linked to nuclear processes, but it is unclear to what degree it is a cause or consequence of function. We aim to understand whether the Nucleosome Remodeling and Deacetylation (NuRD) complex regulates chromatin structure to control transcription, or whether it is NuRD’s regulation of transcription that results in global changes in chromosome structure. We have calculated the first 3D structures of entire mammalian genomes using a new chromosome conformation capture procedure, which combines imaging with Hi-C processing of the same single cell. Our objectives are now: • To study: 1) how interphase mammalian genome structure is established in G1; 2) the factors that drive this formation and; 3) how this organisation is regulated by chromatin remodellers (such as the NuRD complex) as mESC’s differentiate. • To build a dedicated bespoke microscope for 3D double helix point spread function detection with light sheet activation, optimised for 3D single-molecule/super-resolution imaging of proteins such as the NuRD complex. • To combine 3D super-resolution imaging and the biochemical processing steps of single cell Hi-C to directly correlate binding of protein complexes to regions of the structures.

Lay abstract: The Nucleosome Remodeling and Deacetylation (NuRD) protein complex is thought to play a key role in controlling the way our genomes are packaged inside the cell, and whether particular genes (sequences of DNA) are/are not expressed. In particular, the NuRD complex controls gene expression as embryonic stem (ES) cells first start to differentiate into all the different types of cells in the body. We envisage a highly inter-disciplinary research program to study the structures of intact genomes in single cells, how genome structure is controlled by the NuRD complex, and how this changes during the early stages of differentiation. Our long-term goal is to use this understanding to control the differentiation of stem cells. This understanding when applied to either ES cells, or adult cells that have been induced to become stem cells (iPS cells), could have enormous potential – e.g. for providing a source of human tissue to study disease progression, or to develop drugs for personalised molecular therapies. We will also investigate small molecule inhibitors of the NuRD complex to control chromatin structure. Our research may in the long-term facilitate our ability to directly influence gene expression profiles, stem cell differentiation and disease.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Integrative structural biology of protein folding during biosynthesis on the ribosome
Funder: Wellcome Trust

Abstract: Central to the activity of all living systems is the need for polypeptide chains to acquire their biologically-active structures and avoid the competing events of misfolding. It is well established that the majority of proteins begin to acquire structure as highly-dynamic nascent chains during biosynthesis on the cell’s protein biosynthesis machinery, the ribosome. A detailed molecular understanding of how this native structure is acquired and how misfolding is avoided during biosynthesis is sparse. We will build on our capacity to derive structural and dynamic mechanistic information of the fundamental process of co-translational folding: we will produce a multi-scalar analysis extending from in vitro to in vivo to provide a comprehensive, high-resolution description of emerging nascent chains (NC) during biosynthesis. Our research will integrate NMR and cryo-EM to answer emerging questions regarding the observation that the ribosome itself can modulate folding processes, and also act as a hub for the recruitment and co-ordination of auxiliary proteins that can assist NC folding and modification processes. Structure-based design, incorporating protein engineering and ribosome modification will dissect NC folding mechanisms and understand how misfolding is avoided. This underpins aims to reshape co-translational folding, targeting the ribosome and NC at the earliest stages of protein-biosynthesis.

Lay abstract: In all cells, the ribosome is the molecular machine that manufactures proteins from information encoded within our DNA. Proteins are synthesized as a chain of amino-acids built one at a time, and must acquire (or “fold”) their particular shape(“structure”) for them to function; failure to fold(“misfolding”) can have devastating consequences, and implicated in many diseases including neurodegeneration and some cancers. During protein synthesis, the ribosome appears to have a key role in guiding folding of nascent proteins before they are released into the cell’s environment. Despite a wealth of information on the ribosome's ability to form peptides, the understanding of the protein folding processes on the ribosome remains sparse. We aim to transform this understanding by applying recently developed genetic-engineering methods to capture different stages of protein synthesis on the ribosome. Together with atomic-level visualisation methods we will analyse this series of “3D-snapshots” to describe how the ribosome guides nascent protein folding. This has important ramifications for understanding why folding can fail and how this is dealt with by the cell. Armed with this information, we can then design ways to manipulate the process (e.g.through novel antibiotics,antibodies) to target the nascent protein or ribosome to re-configure protein-folding and avoid misfolding.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Proton coupled transporters in health and disease.
Funder: Wellcome Trust

Abstract: Proton coupled transporters play important roles in human health and disease, being responsible for the uptake and distribution of nutrients into the body and between organs, regulating metabolism and impacting the pharmacokinetic profiles of orally administered drug molecules. Remarkably, given their importance in cell biochemistry, little is understood regarding their structure, mechanism of action or regulation. This proposal seeks to close this gap in our knowledge. Using a combination of structural, biochemical and biophysical approaches I will determine the molecular basis for ligand recognition, transport and regulation within the peptide (SLC15), amino acid (SLC36) and folate (SLC46) transporter families. This research will establish the mechanism by which these proteins transport nutrients and drug molecules into the cell and across organellular membranes, facilitating a more rational strategy to improve drug uptake and retention in the human body. My key goals are: • Determine the molecular basis for proton coupled nutrient and drug transport into eukaryotic cells. • Develop accurate pharmacophore models that explain how drug molecules are recognised and translocated across membranes. • Reveal the mechanisms that regulate these systems in different membrane environments and organelles. • Engage with the pharmaceutical industry to advance drug design and delivery within the human body.

Lay abstract: This research will explain how drugs enter the human body and target specific organs. In humans many of the systems responsible for absorbing nutrients from our diet, such as protein, fat, vitamins and sugars are also responsible for the uptake of tablet based medicines, such as antibiotics, antiviral and anticancer drugs. Many medicines however are not as effective as they could be; often the result of poor intestinal absorption or rapid breakdown and excretion in our urine. My research aims to advance our understanding of how drugs enter our body and target them to specific sites of disease. Using a combination of advanced imaging techniques this proposal will reveal how these proteins recognise drug molecules and provide a blueprint to improve their effectiveness. The insights revealed will advance our understanding of basic cell biochemistry and enable a range of more efficient antivirals, antibiotics and chemotherapy agents to be developed.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: The Molecular Basis of Sister Chromatid Cohesion
Funder: Wellcome Trust

Abstract: Cohesion between sister chromatids, mediated by the chromosomal cohesin complex, is a prerequisite for faithful chromosome segregation during cell division. The ring-shaped cohesin complex is a multisubunit ATPase that topologically loads onto DNA in the G1 phase of the cell cycle. The first part of the proposal will elucidate the molecular mechanism of cohesin function. We will employ and develop biophysical, structural and DNA-protein crosslink mass spectrometry tools to map the trajectory by which DNA enters the cohesin ring, fuelled by ATP-dependent conformational changes. The second part of the proposal examines the establishment of sister chromatid cohesion during S phase. We will investigate how, as the replication fork moves along DNA, cohesin transitions from containing one DNA to embracing two newly replicated DNAs. This includes the functional characterisation of replisome components with roles in sister chromatid cohesion, known as ‘cohesion establishment factors’. Furthermore, we will take advantage of recent success with the biochemical reconstitution of complete DNA replication and work towards recapitulating sister chromatid cohesion establishment in vitro. This will open unique experimental opportunities to understand the process. Together, this programme will provide insight into the molecular mechanism of how cohesin safeguards faithful chromosome segregation.

Lay abstract: The description of chromosome segregation during cell division reaches back over a century. Abnormal chromosome counts correlate with human malignancies and, already in 1890, Hansemann suggested that aberrant chromosome segregation causes the aberrant behaviour of cancer cells. Meanwhile, we know that replicated sister chromatids are held together by the ring-shaped cohesin complex, forming the basis for their faithful pairwise segregation during cell division. Cohesin topologically embraces sister DNAs, but how does DNA enter cohesin rings? Most importantly, how does cohesin tether exactly the two DNA replication products that are produced in S phase? Here, we propose to innovate molecular experimental tools to answer these central outstanding questions. We will take advantage of recent advances to recapitulate both topological cohesin loading onto DNA, as well as DNA replication, with purified proteins. This will help us understand the process by which cells faithfully pass on chromosomes to their daughters.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: How filopodia form
Funder: Wellcome Trust

Abstract: Filopodia are finger-like actin rich projections from cells that are ubiquitously present during cell movement, are involved in cell connectivity, and are hijacked for internalization by pathogens. We established a cell-free system of filopodia-like structure formation using supported lipid bilayers and frog egg extracts, which has generated hypotheses about where and when filopodia form. My first aim is to discover how endocytosis and phosphoinositide lipid metabolism contribute to the time and place of filopodia formation and suppression in retinal ganglion cell neurons. We will examine the timing and contributions of neurotrophic factor signalling through PI(4,5)P2, PI(3,4,5)P3, PI(3,4)P2 and PI(3)P to membrane deformation and filopodial protrusion. We will explore filopodia in axon guidance, terminal arborization and synaptogenesis, and recovery from neuronal injury. My second aim is to identify the proteins needed for formation of filopodia-like structures to increase our understanding of the molecular mechanisms that determine filopodia function in cells. Where filopodia form determines the direction of cell movement, their length determines the extent of signal sensitivity and their lifetime determines the strength of signaling or duration of migration and adhesion. Our molecular and cellular studies may also give us information needed to manipulate actin regulation therapeutically.

Lay abstract: The ability of cells to sense their environment and move towards stimuli underlies embryonic development and the origin of multicellular life. Finger-like actin-rich protrusions, known as filopodia, are ubiquitous organelles of cell sensing and migration that are also involved in cell connectivity and tissue architecture. We will use biochemical and microscopic methods to understand the molecular mechanisms upon which filopodia carry out their functions. Using a unique cell-free system where filopodia-like structures can be generated, we will identify key filopodia proteins and regulators, and aim to reconstitute these structures from known purified components. In a cellular context, we will explore how membrane and actin dynamics give rise to filopodia in particular places and times in neurons. Unravelling the fundamental mechanisms of filopodial dynamics will lead to a wider understanding of the myriad ways filopodia function in biology.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE