Understanding the Structural and Functional Importance of Early Folding Residues in Protein Structures

Proteins adopt three-dimensional structures which serve as a starting point to understand protein function and their evolutionary ancestry. It is unclear how proteins fold in vivo and how this process can be recreated in silico in order to predict protein structure from sequence. Contact maps are a possibility to describe whether two residues are in spatial proximity and structures can be derived from this simplified representation. Coevolution or supervised machine learning techniques can compute contact maps from sequence: however, these approaches only predict sparse subsets of the actual contact map. It is shown that the composition of these subsets substantially influences the achievable reconstruction quality because most information in a contact map is redundant. No strategy was proposed which identifies unique contacts for which no redundant backup exists. The StructureDistiller algorithm quantifies the structural relevance of individual contacts and identifies crucial contacts in protein structures. It is demonstrated that using this information the reconstruction performance on a sparse subset of a contact map is increased by 0.4 A, which constitutes a substantial performance gain. The set of the most relevant contacts in a map is also more resilient to false positively predicted contacts: up to 6% of false positives are compensated before reconstruction quality matches a naive selection of contacts without any false positive contacts. This information is invaluable for the training to new structure prediction methods and provides insights into how robustness and information content of contact maps can be improved. In literature, the relevance of two types of residues for in vivo folding has been described. Early folding residues initiate the folding process, whereas highly stable residues prevent spontaneous unfolding events. The structural relevance score proposed by this thesis is employed to characterize both types of residues. Early folding residues form pivotal secondary structure elements, but their structural relevance is average. In contrast, highly stable residues exhibit significantly increased structural relevance. This implies that residues crucial for the folding process are not relevant for structural integrity and vice versa. The position of early folding residues is preserved over the course of evolution as demonstrated for two ancient regions shared by all aminoacyl-tRNA synthetases. One arrangement of folding initiation sites resembles an ancient and widely distributed structural packing motif and captures how reverberations of the earliest periods of life can still be observed in contemporary protein structures

Uncovering the Roles and Evolved Sequence Grammar of Hypervariable Intrinsically Disordered Proteins in Bacterial Cell Division

Across all domains of life, a defining hallmark of the onset of cell division is the formation of a cytokinetic ring at the center of the cell. Cell division is a tightly controlled process that involves various regulatory factors that modulate the assembly of the cytokinetic ring. In rod-shaped bacteria, the ring is termed the Z-ring after the protein FtsZ, which is foundational to ring formation and is the bacterial homolog of tubulin. Like tubulin, FtsZ is an assembling GTPase, where GTP binding promotes the cooperative assembly into FtsZ polymers that laterally associate to form bundles. While the GTPase domain drives FtsZ polymerization, the formation of these higher-order structures requires domains outside the folded core. FtsZ has a bristled architecture, where a disordered tail, called the C-terminal tail (CTT), flanks the folded domain. The essentiality of the CTT was established through deletion experiments; however, the exact role that the CTT plays within the context of FtsZ function remained unclear. Here, we establish that the CTT, containing an intra-and intermolecular interaction motif (CTP) and a disordered linker (CTL), has a sticker-and-spacer architecture, where the CTL modulates the interactions of the CTP. We find that the modules of the CTT not only influence FtsZ assembly but also impact the catalytic efficiency of the GTPase domain. These findings add to recent findings that implicate disordered regions tethered to enzymes in auto-regulatory activities. The findings summarized above were obtained by focusing our investigations on the CTT of the FtsZ protein from B. subtilis (Bs-FtsZ). Is the stickers-and-spacers model applicable to understanding the functions of CTTs from other bacterial FtsZs? We analyzed the sequences of 1208 orthologous FtsZs, and the results show that while the CTPs and the core domains are reasonably well conserved, the CTLs are hypervariable across orthologs. The results of the sequence analysis have several implications: It might reflect a form of convergent evolution whereby different CTL sequences are interoperable with one other because different sequences serve the functionality of being spacers. Alternatively, the variation could be an example of divergent evolution, whereby changes to the CTLs engender different functionalities in different bacteria. Answering these questions will require methods to identify common sequence patterns across orthologous CTLs, and this cannot be achieved using traditional multiple sequence alignment approaches. Accordingly, we introduce computational methods that enable the quantitative analysis of conserved / distinct sequence-ensemble relationships across a family of IDRs. Additionally, we introduce a new method to uncover cryptic sequence patterns that define disordered regions as random versus non-random. These methods are shown to be applicable for high-throughput analysis of CTLs derived from different FtsZs. They are also effective in uncovering sequence patterns that are cryptic but conserved in intrinsically disordered regions (IDRs) from other bacterial proteins. Given the role of sequence-ensemble relationships and non-random motifs in IDP/IDR function, we hypothesized that these features might influence function and, therefore, might be encoded for within the amino acid sequence of the FtsZ CTL. This implies that designed CTL sequence variants that result in significant changes to these sequence features and to the ability of the CTL to function as a spacer could perturb function. To test this hypothesis, we developed scrambled sequence variants of the B. subtilis FtsZ CTL using the patterning of oppositely charged residues as a design parameter. Leveraging new methodologies, we found that the designed variants caused changes to the sequence-ensemble relationships, the non-random sequence patterning, and / or the spacer properties. Each variant was tested for complementary functions to wild type in vitro and in vivo. Indeed, deviations from wild type features had phenotypic impacts and / or influenced FtsZ assembly and activity, showing that the CTL is not a random disordered sequence but instead has specifically encoded sequence features that dictate function. As the global need to combat antibiotic-resistant infections continues to mount, studies that further understand the functions that IDRs contribute to essential bacterial processes such as cell division can be leveraged to create next-generation antibiotics

Informatics for Health 2017 : advancing both science and practice

Conference report, The Informatics for Health congress, 24-26 April 2017, in Manchester, UK.Introduction : The Informatics for Health congress, 24-26 April 2017, in Manchester, UK, brought together the Medical Informatics Europe (MIE) conference and the Farr Institute International Conference. This special issue of the Journal of Innovation in Health Informatics contains 113 presentation abstracts and 149 poster abstracts from the congress. Discussion : The twin programmes of “Big Data” and “Digital Health” are not always joined up by coherent policy and investment priorities. Substantial global investment in health IT and data science has led to sound progress but highly variable outcomes. Society needs an approach that brings together the science and the practice of health informatics. The goal is multi-level Learning Health Systems that consume and intelligently act upon both patient data and organizational intervention outcomes. Conclusions : Informatics for Health demonstrated the art of the possible, seen in the breadth and depth of our contributions. We call upon policy makers, research funders and programme leaders to learn from this joined-up approach.Publisher PDFPeer reviewe

Person-Centered Outcome Metrology

This unique collection of chapters from world experts on person-centered outcome (PCO) measures addresses the following critical questions: Can individual experiences be represented in measurements that do not reduce unique differences to meaningless uniformity? How person-centric are PCO measures? Are PCO measurements capable of delivering the kind of quality assured quantification required for high-stakes decision making? Are PCO measures likely to support improved health care delivery? Have pivotal clinical studies failed to deliver treatments for diseases because of shortcomings in the PCO measures used? Are these shortcomings primarily matters of precision and meaningfulness? Or is the lack of common languages for communicating outcomes also debilitating to quality improvement, research, and the health care economy? Three key issues form an urgent basis for further investigation. First, the numbers generated by PCO measures are increasingly used as the central dependent variables upon which high stakes decisions are made. The rising profile of PCO measures places new demands for higher quality information from scale and test construction, evaluation, selection, and interpretation. Second, PCO measurement science has well-established lessons to be learned from those who have built and established the science over many decades. Finally, the goal in making a PCO measurement is to inform outcome management. As such, it is vitally important that key stakeholders understand that, over the last half century, developments in psychometrics have refocused measurement on illuminating clinically important individual differences in the context of widely reproduced patterns of variation in health and functioning, comparable scale values for quality improvement, and practical explanatory models. This book’s audience includes anyone interested in person-centered care, including healthcare researchers and practitioners, policy makers, pharmaceutical industry representatives, clinicians, patient advocates, and metrologists. This is an open access book

Person-Centered Outcome Metrology

This unique collection of chapters from world experts on person-centered outcome (PCO) measures addresses the following critical questions: Can individual experiences be represented in measurements that do not reduce unique differences to meaningless uniformity? How person-centric are PCO measures? Are PCO measurements capable of delivering the kind of quality assured quantification required for high-stakes decision making? Are PCO measures likely to support improved health care delivery? Have pivotal clinical studies failed to deliver treatments for diseases because of shortcomings in the PCO measures used? Are these shortcomings primarily matters of precision and meaningfulness? Or is the lack of common languages for communicating outcomes also debilitating to quality improvement, research, and the health care economy? Three key issues form an urgent basis for further investigation. First, the numbers generated by PCO measures are increasingly used as the central dependent variables upon which high stakes decisions are made. The rising profile of PCO measures places new demands for higher quality information from scale and test construction, evaluation, selection, and interpretation. Second, PCO measurement science has well-established lessons to be learned from those who have built and established the science over many decades. Finally, the goal in making a PCO measurement is to inform outcome management. As such, it is vitally important that key stakeholders understand that, over the last half century, developments in psychometrics have refocused measurement on illuminating clinically important individual differences in the context of widely reproduced patterns of variation in health and functioning, comparable scale values for quality improvement, and practical explanatory models. This book’s audience includes anyone interested in person-centered care, including healthcare researchers and practitioners, policy makers, pharmaceutical industry representatives, clinicians, patient advocates, and metrologists. This is an open access book