Browsing Biological chemistry by Subject "Biological chemistry"
Now showing items 1-20 of 80
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A Hierarchical Approach to the Design of Protein Crystals
Despite the fact that scientists have been using X-ray crystallography for the structure determination of proteins for nearly 80 years, understanding and controlling the crystallization of proteins has remained an outstanding ... -
Actin-like filament A (AlfA) and AlfA-driven plasmid segregation
For a long time, the cytoskeleton was considered an exclusive feature of eukaryotic cells. In 1992, it was proposed that bacteria might contain actin and tubulin homologs. Cell biology and structural biology research within ... -
Advances In Computer Aided Protein Structure Determination From Sparse Cryo Electron Microscopy Data
Single-particle cryo-electron microscopy (cryoEM) has become a powerful tool for determining macromolecular structures. Thanks to recent advances in direct electron detectors and motion correction algorithms it can frequently ... -
Aminoacyl-tRNA Synthetases as Targets for Structure Guided Drug Design (SGDD) Against Pathogenic Protozoa and Bacteria
Tuberculosis (TB) and neglected tropical diseases (NTDs) caused by trypanosomatids are devastating diseases affecting millions of people around the globe. Mycobacterium tuberculosis causes TB, while the trypanosomatids ... -
An Interdisciplinary Investigation of Conformational Changes in Quasi-Crystalline Protein Array R-bodies in Response to pH
R-bodies are ribbon-like protein polymers that undergo a dramatic conformational change from a tightly coiled form at neutral pH to an extended helical spiral at acidic pH. R-bodies were found in bacterial endosymbionts ... -
An organelle with many jobs: Mitochondrial specialization in the retina and RPE
The eye is a complex organ with many tissue and cell types working together to facilitate vision. Photoreceptor cells in the retina initiate vision, converting light into a neuronal signal that is integrated and used to ... -
Beyond single-protein de novo design: A generative algorithm for the NTF2-like superfamily
Natural proteins evolved over billions of years to regulate cellular growth, ward off infection and capture and store solar energy. Proteins thus serve as the molecular basis for life. The promise of protein design is to ... -
BRCA1/BARD1-Dependent Ubiquitylation of Nucleosomal Histone H2A
Breast cancer type-1 susceptibility protein (BRCA1) was the first gene to be linked to heritable breast and ovarian cancer over thirty years ago. Since then, remarkable progress has been made with regards to genetic testing, ... -
Building a Functional Kinetochore: From Microtubule to Centromere
Equal partitioning of duplicated chromosomes between daughter cells is a microtubule- mediated process essential to eukaryotic life. A multi-protein machine, the kinetochore, tethers chromosomes to dynamic microtubule tips, ... -
Ca2+ handling and stress responses of photoreceptor mitochondria
Maintenance of mitochondrial function and integrity is essential for cellular health. Mitochondria play key roles in ATP generation, cellular signaling, and control of cell death. These functions are linked to mitochondrial ... -
Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors
Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens ... -
Computational de-novo design of ester hydrolases
(2013-02-25)Computational protein design is a relatively new technique used to devise amino acid sequences to fold into proteins having novel structures or functions. Here, we first give an overview about the approaches and algorithms ... -
Computational Design and Enhancement of Proteins: A Study on Mechanostability and Isopeptide Generation
This study employs de novo protein design to augment protein mechanostability, a critical characteristic in bioengineering, biotechnology, and therapeutic development. The enhancement of protein mechanostability may find ... -
Computational Design of Hyperstable, De Novo Miniproteins Targeting PD-1
Computational protein design has recently advanced to a new era with the de novo design of stable proteins targeting native protein ligands. In this dissertation, I will present the first de novo protein binder with an all ... -
Computational Design of Peptides and Proteins for Cyclic Peptide Applications
Cyclic peptides are a fascinating class of compounds to use in multiple design applications due to their small size and ability to be chemically synthesized. Non-canonical amino acids can be easily incorporated into cyclic ... -
Computational Design of Proteins that Bind to TLR7 and FCyRIIa
TLR7 and FCyRIIa are common immune targets for adjuvant design because they elicit increased activation in TH1 and phagocytosis respectively. With the new wave of computational design tools including RF Diffusion, ProteinMPNN, ... -
Computational Design of Symmetric Protein Complexes with Implications for Vaccine and Biotherapeutic Development
Using a newly developed computational docking and scoring method combined with Rosetta two-sided interface design, we demonstrated accurate design of self-assembling oligomeric proteins that exhibit various degrees of ... -
Conditional Generation of Protein Sequence and Structure
The advent of atomic accuracy protein sequence structure prediction with deep learning networks spurred by AlphaFold has had a remarkable impact on the field of biochemistry. It has resulted in rapid progress in protein ... -
De Novo Design of Bioactive Protein Switches, and Applications Thereof
Allosteric regulation of protein function is widespread in biology, but challenging for de novo protein design as it requires explicit design of multiple states with comparable free energies. We explore the possibility of ... -
De Novo Design of Buttressed Loops for Diversifying Protein Functions
Loops play essential roles in protein functions such as protein-protein interactions, ligand recognition and metal binding. However, designing structured and functional loops remains to be a long-standing challenge for ...