Understanding and Exploiting Protein Allostery and Dynamics Using Molecular Simulations

Protein conformational landscapes contain much of the functionally relevant information that is useful for understanding biological processes at the chemical scale. Understanding and mapping out these conformational landscapescan provide valuable insight into protein behaviors and biological phenomena, and has relevance to the process of therapeutic design. While structural biology methods have been transformative in studying protein dynamics, they are limited by technicallimitations and have inherent resolution limits. Molecular dynamics (MD) simulations are a powerful tool for exploring conformational landscapes, and provide atomic-scale information that is useful in understanding protein behaviors. With recent advances in generating datasets of large timescale simulations (using Folding@home) and powerful methods to interpret conformational landscapes such as Markov State Models (MSMs), it is now possible to study complex biological phenomena and long-timescale processes. However, inferring communication between residues across long distances, referred to as allosteric communication, remains a challenge. Allostery is a ubiquitious biological phenomena by which two distant regions of a protein are coupled to one anotherover large distances. Allosteric coupling is the mechanism through which events in one region (such as ligand binding) alter the conformation or dynamics of another region (ie. large conformational domain motions). For example, allostery plays a critical role in cellular signaling, such as in the transfer of a signal from outside the cell to cytosolic proteins for generating a cellular response. While many methods have made tremendous progress in inferring and measuring allosteric communication usingstructures or molecular simulations, they rely on a structural view of allostery and do not account for the role of conformational entropy. Furthermore, it remains a challenge to interpret allosteric coupling in large, complex biomolecules relevant to physiology and disease. In this thesis, I present a method to measure the Correlation of All Rotameric and Dynamical States (CARDS) whichis used to construct and interpret allosteric networks in biological systems. CARDS allows us to infer allostery both via concerted changes in protein structure and in correlated changes in conformational entropy (dynamic allostery). CARDS does so by parsing trajectories into dynamical states which reflect whether a residue is locally ordered (ie. stable in a single rotameric basin) or disordered (ie. rapidly hopping between rotamers). Here I explain the CARDS methodology (chapter 2) and demonstrate applications to a variety of disease-relevantsystems. In particular, I apply CARDS and other sophisticated computational methods to understand the process of G protein activation (chapter 3), a protein whose mutations are linked to cancers such as uveal melanoma. I further demonstrate the utility of CARDS in the study a potentially druggable pocket in the ebolavirus protein VP35 (chapter 4). The analyses and models constructed in this work are supported by experimental testing. Lastly, I demonstrate how integrating MD with experiments, sometimes with the help of citizen-scientists around the world, can provide unique insight into biological systems and identify potentially useful targets. In particular, I highlight our recent effort converting Folding@home into an exascale computer platform to hunt for potentially druggable pockets in the proteome of SARS-CoV-2 (chapter 7) (the cause of the COVID19 pandemic)

Clinical, genetic and molecular aspects of membranous nephropathy

Membranous Nephropathy (MN) is one of the leading causes of end-stage renal disease (ESRD). MN is an autoimmune disease in which autoantibodies target antigens at the level of the glomerular basement membrane. The nature of these antibodies and the reason why they develop are not fully understood. One of the strategies towards a better understanding of the disorder is genetic analysis, of which two approaches have been attempted: linkage mapping, based on a family suggestive for X-linked transmission of the MN trait; and whole genome association mapping, based on three case-control cohorts. The first cohort (335 cases and ethnically matched controls from the UK) was genotyped using SNP markers and analysed in an exploratory study which led to the identification of two highly significant loci of association. Two cohorts (146 biopsy proven MN cases and ethnically matched controls from the Dutch research group in Nijmegen and 75 biopsy proven cases and ethnically matched controls from the French research group in Paris) were used to successfully replicate the results. The two loci which we identified and independently confirmed are located on chromosome 2 and on chromosome 6. The chromosome 2 locus includes the PLA2R gene, confirming the hypothesis of Beck et al. which identified PLA2R as a key antigen in idiopathic MN by using an immunological approach [1]. The chromosome 6 locus lies within the extended Human Leukocyte Antigene (HLA) system locus, with the highest significance for association reached by alleles of HLA-DQA1. Our results suggest that the susceptibility to membranous nephropathy is associated to genetic variants at the level of both PLA2R1 and HLA loci. The causative variants could be some of the polymorphisms captured by the genotyping array which was analysed or, more likely variants (single nucleotide or copy number variant type) situated nearby (and therefore in linkage disequilibrium)

Plant Science

The book "Plant Science" consists of 12 chapters divided into three sections authored by many researchers from different parts of the Globe. Section-I: Plant and Environment, describes the relationship between plants and environment, particularly enumerating species-environment relationship and response of plants to different environmental stress conditions. Section-II: Plant-Microbe relation, embodies broadly on both positive and negative aspects of microbes on plants. Section-III: Plant Biotechnology, shed light on current biotechnological research to develop modern technology for producing biologicals and also increasing plant immunity in present environmental conditions. The book "Plant Science" will be helpful to a wide group peoples; readers, scientists, researchers and allied professionals. We recommend it to you; enjoy reading it, save the plant and save life

Chromatin-based memory of prolonged cold exposure in Arabidopsis thaliana

All living organisms contain genes. Turning these genes on and off at the appropriate times controls much of an organism’s development and its responses to environmental conditions. In recent years, chromatin has emerged as an important player in orchestrating gene regulation. This thesis focuses on the role of chromatin in the maintenance of gene expression states and their inheritance through cell division. FLOWERING LOCUS C (FLC) in the plant Arabidopsis thaliana is repressed by the prolonged cold of winter, and repression is maintained in subsequent warm conditions. The molecular complexes involved in modulating FLC chromatin are vital for FLC regulation and are conserved among plants and animals, making FLC a paradigmatic system for understanding of the role of chromatin in gene regulation. After cold, FLC chromatin adopts a distinct configuration. In this study, experiments are used to show that this local chromatin ‘state’ instructs its own inheritance through cell division in growing plants. Thus, memory of winter cold is stored in the chromatin of the FLC gene. Mathematical models developed in this work focus on understanding how chromatin states are maintained and also re-established after DNA replication. Minimal models are used to investigate if a particular set of interactions between chromatin and chromatin-modifiers can give rise to the qualitative behaviours, and quantitative results that are observed experimentally. Models developed here make predictions for the FLC system, and more generally show how cis and trans determinants of gene expression can be integrated by chromatin. The role of transcription in determining chromatin states is also examined experimentally by studying the chromatin-associated protein LHP1. LHP1 is required for FLC repression and binds to modified histones associated with repressed FLC chromatin. In this work, it is shown that LHP1 also binds RNA and that this is important for its in vivo function

A complex systems approach to education in Switzerland

The insights gained from the study of complex systems in biological, social, and engineered systems enables us not only to observe and understand, but also to actively design systems which will be capable of successfully coping with complex and dynamically changing situations. The methods and mindset required for this approach have been applied to educational systems with their diverse levels of scale and complexity. Based on the general case made by Yaneer Bar-Yam, this paper applies the complex systems approach to the educational system in Switzerland. It confirms that the complex systems approach is valid. Indeed, many recommendations made for the general case have already been implemented in the Swiss education system. To address existing problems and difficulties, further steps are recommended. This paper contributes to the further establishment complex systems approach by shedding light on an area which concerns us all, which is a frequent topic of discussion and dispute among politicians and the public, where billions of dollars have been spent without achieving the desired results, and where it is difficult to directly derive consequences from actions taken. The analysis of the education system's different levels, their complexity and scale will clarify how such a dynamic system should be approached, and how it can be guided towards the desired performance

Stinging the Predators: A collection of papers that should never have been published

This ebook collects academic papers and conference abstracts that were meant to be so terrible that nobody in their right mind would publish them. All were submitted to journals and conferences to expose weak or non-existent peer review and other exploitative practices. Each paper has a brief introduction. Short essays round out the collection

Laboratory Directed Research and Development Annual Report - Fiscal Year 2000

The projects described in this report represent the Laboratory's investment in its future and are vital to maintaining the ability to develop creative solutions for the scientific and technical challenges faced by DOE and the nation. In accordance with DOE guidelines, the report provides, a) a director's statement, b) an overview of the laboratory's LDRD program, including PNNL's management process and a self-assessment of the program, c) a five-year project funding table, and d) project summaries for each LDRD project