Browsing Biological chemistry by Title
Now showing items 5-24 of 122
-
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 ... -
Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex
The evolutionarily conserved transcription coactivator SAGA (Spt-Ada-Gcn5 Acetyltransferase) is a multi-subunit complex with a modular structure, which has several distinct activities that are used to regulate activator-dependent ... -
Assessing and Improving Computational Models of Protein Thermodynamics and Kinetics
(2013-04-17)The purpose of this thesis is to rigorously assess and improve computational models of protein thermodynamics and kinetics. The first part consists of computational ddG prediction; we explore the performance of protocols ... -
Autophagy, or not to be: The delicate balance of cellular self-digestion in neurons and neurodegeneration
(2013-04-17)Neurons rely on autophagy for some critical functions, perhaps even more so than non-neuronal cells [4], but the process does not have such a clear-cut role in these cells. In some cases, autophagy can assist the cell by ... -
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 ... -
Biophysical mechanisms of the kinetochore-microtubule interface and its regulation during mitosis
Chromosomes carry the genetic information that acts as a "blueprint" for every organism. When cells divide, replicated copies of the chromosomes are segregated into two new cells that are genetic copies of the original. ... -
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 ... -
Characterizing and modulating the canine T-cell costimulatory molecules CTLA-4 and CD28
Current treatments for graft versus host disease, a major side effect of hematopoietic stem cell transplantation, have serious harmful side effects. The complexity of the cellular mechanisms leading to effector T-cell ... -
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 Protein Therapeutics with Reduced Immunogenicity through Structural Modeling of Protein Interactions
(2014-04-30)Proteins possess huge potential as therapeutic agents for the control and modulation of human physiology. Protein interactions regulate most physiological processes, mediating the connection between atomic-scale self-assembly ... -
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 ...