Amino Acids, Peptides, and Proteins Commons^™

Bone Morphogenetic Proteins Shape TReg Cells, Piotr Kraj

Biological Sciences Faculty Publications

The transforming growth factor-β (TGF-β) family includes cytokines controlling cell behavior, differentiation and homeostasis of various tissues including components of the immune system. Despite well recognized importance of TGF-β in controlling T cell functions, the immunomodulatory roles of many other members of the TGF-β cytokine family, especially bone morphogenetic proteins (BMPs), start to emerge. Bone Morphogenic Protein Receptor 1α (BMPR1α) is upregulated by activated effector and Foxp3+ regulatory CD4+ T cells (Treg cells) and modulates functions of both of these cell types. BMPR1α inhibits generation of proinflammatory Th17 cells and sustains peripheral Treg cells. This finding underscores the importance of …

The Benefit Of Bdnf Modification In The Treatment Of Post-Stroke Depression, Christine Gordynskiy-Ageyev

Capstone Showcase

Neuroplasticity has been a rapidly expanding area of research, and its findings have elucidated the potential of taking advantage of some of its components for the treatment of various neural pathologies. Stroke is the most common cause of long-term disability, and it is a disease process that affects many people. There are many rehabilitation programs that seek to restore a patient’s motor and cognitive functions after stroke; if not fully, then at least partially. Unfortunately, mental health changes contribute in large part to the overall disability of a patient, but these changes are not always targeted in these programs. In …

Protein Structure And Interaction: The Role Of Aromatic Residues In Protein Structure And Interactions Between Pyridoxine 5'-Phosphate Oxidase/Dopa Decarboxylase, Mohammed H. Al Mughram

Theses and Dissertations

Naturally developed proteins are capable of carrying out a wide variety of molecular functions due to their highly precise three-dimensional structures, which are determined by their genetically encoded sequences of amino acids. A thorough knowledge of protein structures and interactions at the atomic level will enable researchers to get a deep foundational understanding of the molecular interactions and enzymatic processes required for cells, resulting in more effective therapeutic interventions. This dissertation intends to use structural knowledge from solved protein structures for two distinct objectives.

In the first project, we conducted a bioinformatics structural analysis of experimental protein structures using our …

The Landscape Of Accessible Chromatin In Quiescent Cardiac Fibroblasts And Cardiac Fibroblasts Activated After Myocardial Infarction, Chaoyang Yi, Jiangwen Sun, Qianglin Liu, Sanjeeva Dodlapati, Hao Ming, Leshan Wang, Yuxia Li, Rui Li, Zongliang Jiang, Joseph Francis, Xing Fu

Computer Science Faculty Publications

After myocardial infarction, the massive death of cardiomyocytes leads to cardiac fibroblast proliferation and myofibroblast differentiation, which contributes to the extracellular matrix remodelling of the infarcted myocardium. We recently found that myofibroblasts further differentiate into matrifibrocytes, a newly identified cardiac fibroblast differentiation state. Cardiac fibroblasts of different states have distinct gene expression profiles closely related to their functions. However, the mechanism responsible for the gene expression changes during these activation and differentiation events is still not clear. In this study, the gene expression profiling and genome-wide accessible chromatin mapping of mouse cardiac fibroblasts isolated from the uninjured myocardium and the …

Refinement Of Alphafold2 Models Against Experimental And Hybrid Cryo-Em Density Maps, Maytha Alshammari, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Recent breakthroughs in deep learning-based protein structure prediction show that it is possible to obtain highly accurate models for a wide range of difficult protein targets for which only the amino acid sequence is known. The availability of accurately predicted models from sequences can potentially revolutionise many modelling approaches in structural biology, including the interpretation of cryo-EM density maps. Although atomic structures can be readily solved from cryo-EM maps of better than 4 Å resolution, it is still challenging to determine accurate models from lower-resolution density maps. Here, we report on the benefits of models predicted by AlphaFold2 (the best-performing …