A5078516822- Protein Structure and Dynamics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Crystallography and molecular interactions
- Ubiquitin and proteasome pathways
- X-ray Diffraction in Crystallography
- Crystallization and Solubility Studies
- Protein Degradation and Inhibitors
- Transgenic Plants and Applications
- CRISPR and Genetic Engineering
- Microbial Metabolic Engineering and Bioproduction
- Endoplasmic Reticulum Stress and Disease
- Viral Infectious Diseases and Gene Expression in Insects
- Genetic Neurodegenerative Diseases
- Monoclonal and Polyclonal Antibodies Research
- Heat shock proteins research
- Evolution and Genetic Dynamics
- Protein purification and stability
- Mass Spectrometry Techniques and Applications
- Mitochondrial Function and Pathology
- Machine Learning in Bioinformatics
- Machine Learning in Materials Science
- Advanced Biosensing Techniques and Applications
- HIV Research and Treatment
- Computational Drug Discovery Methods
University of Copenhagen
2014-2024
Technical University of Denmark
2010
Predicting the thermodynamic stability of proteins is a common and widely used step in protein engineering, when elucidating molecular mechanisms behind evolution disease. Here, we present RaSP, method for making rapid accurate predictions changes by leveraging deep learning representations. RaSP performs on-par with biophysics-based methods enables saturation mutagenesis less than second per residue. We use to calculate ∼ 230 million nearly all single amino acid human proteome, examine...
Abstract Proteostasis can be disturbed by mutations affecting folding and stability of the encoded protein. An example is ubiquitin ligase Parkin, where gene variants result in autosomal recessive Parkinsonism. To uncover pathological mechanism provide comprehensive genotype-phenotype information, variant abundance massively parallel sequencing (VAMP-seq) leveraged to quantify Parkin cultured human cells. The resulting mutational map, covering 9219 out 9300 possible single-site amino acid...
Understanding and predicting how amino acid substitutions affect proteins are keys to our basic understanding of protein function evolution. Amino changes may in a number ways including direct perturbations activity or indirect effects on folding stability. We have analyzed 6,749 experimentally determined variant from multiplexed assays abundance two (NUDT15 PTEN) quantify these find that third the variants cause loss function, about half loss-of-function also low cellular abundance. analyze...
Abstract Intrinsically disordered proteins and regions (collectively IDRs) are pervasive across proteomes in all kingdoms of life, help shape biological functions, involved numerous diseases. IDRs populate a diverse set transiently formed structures, yet defy commonly held sequence-structure-function relationships. Recent developments protein structure prediction have led to the ability predict three-dimensional structures folded at proteome scale, enabled large-scale studies...
Abstract Unstable proteins are prone to form non-native interactions with other and thereby may become toxic. To mitigate this, destabilized targeted by the protein quality control network. Here we present systematic studies of cytosolic aspartoacylase, ASPA, where variants linked Canavan disease, a lethal neurological disorder. We determine abundance 6152 6260 ( ~ 98%) possible single amino acid substitutions nonsense ASPA in human cells. Most low degraded through ubiquitin-proteasome...
The eukaryotic proteome undergoes constant surveillance by quality control systems that either sequester, refold, or eliminate aberrant proteins ubiquitin-dependent mechanisms. Ubiquitin-conjugation necessitates the recognition of degradation determinants, termed degrons, their cognate E3 ubiquitin-protein ligases. To learn about distinctive properties we performed an unbiased peptidome stability screen in yeast. search identify a large cohort proteome-derived some which exhibited broad...
Structural disulfides are very rarely found in cytoplasmic proteins of mesophilic organisms. Nevertheless, can form the cytosol if these stabilized sufficiently by supporting protein structure. To investigate redox properties structural disulfide bonds, we introduced bonds into cytosolic enzyme from E. coli, orotate phosphoribosyl transferase (OPRT). Because OPRT is a homodimer introduction opposing cysteine residues (R44C and D92C) separate monomers meant that bond formation could easily be...
Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as native state globular proteins. Here, we introduce kinetic algorithm, CRISP, that greatly enhances sampling efficiency all-atom MC simulations dense systems. The algorithm based on an exact analytical solution classic chain-closure problem, making possible...
Abstract Background Accurately covering the conformational space of amino acid side chains is essential for important applications such as protein design, docking and high resolution structure prediction. Today, most common way to capture this through rotamer libraries - discrete collections chain conformations derived from experimentally determined structures. The discretization can be exploited efficiently search space. However, discretizing naturally continuous comes at cost losing...
Charges are considered an integral part of protein structure and function, enhancing solubility providing specificity in molecular interactions. We wished to investigate whether charged amino acids indeed required for biogenesis a completely free titratable side chains can maintain solubility, stability, function. As model, we used cellulose-binding domain from Cellulomonas fimi, which, among proteins more than 100 acids, presently is the least Protein Data Bank, with total only four...
We present a new software framework for Markov chain Monte Carlo sampling simulation, prediction, and inference of protein structure. The package contains implementations recent advances in methodology, such as efficient local updates from probabilistic models These form alternative to the widely used fragment rotamer libraries. Combined with an easily extendible architecture, this makes PHAISTOS well suited Bayesian structure sequence and/or experimental data. Currently, two force‐fields...
Dehydration of crystalline solids is a widespread phenomenon, yet the fundamental mechanisms by which dehydration occurs are not properly understood. This arises due to technical limitations in studying such fast processes with sufficient sensitivity; nevertheless, understanding pathways critical for designing optimal properties materials, particularly case pharmaceutical solids. The computational methods presented here allow accurate determination dehydrated species’ crystal structure and...
Effective proteome homeostasis is key to cellular and organismal survival, cells therefore contain efficient quality control systems monitor remove potentially toxic misfolded proteins. Such general protein a large extent relies on the robust delivery of or unfolded proteins ubiquitin-proteasome system. This achieved via recognition so-called degradation motifs-degrons-that are assumed become exposed as result misfolding. Despite their importance, nature sequence properties quality-control...
Electrostatic forces are important for protein folding and favored targets of engineering. However, interactions between charged residues difficult to study because the complex network found in most proteins. We have designed a purposely simple system investigate this problem by systematically introducing individual pairs titratable otherwise free such residues. used constant pH molecular dynamics simulations, NMR spectroscopy, thermodynamic double mutant cycles probe structure energetics...
The identification of amino acid substitutions that both enhance the stability and function a protein is key challenge in engineering. Technological advances have enabled assaying thousands variants single high-throughput experiment, more recent studies use such data We present Global Multi-Mutant Analysis (GMMA) exploits presence multiply-substituted to identify individual are beneficial for across large library variants. applied GMMA previously published experiment reporting on >54,000...
Abstract Predicting the thermodynamic stability of proteins is a common and widely used step in protein engineering, when elucidating molecular mechanisms behind evolution disease. Here, we present RaSP, method for making rapid accurate predictions changes by leveraging deep learning representations. RaSP performs on-par with biophysics-based methods enables saturation mutagenesis less than second per residue. We use to calculate ∼ 300 million nearly all single amino acid human proteome,...
The crystal structure of the title compound, C11H13N3O2S2, has been determined previously on basis refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison measured and calculated (13)C solid-state NMR spectra [Hangan et al. (2010). Acta Cryst. B66, 615-621]. molecule is tautomeric, was reported as an amine tautomer [systematic name: N-(5-ethyl-1,3,4-thiadiazol-2-yl)-p-toluenesulfonamide], rather than correct imine tautomer. protonation site molecule's...
The cis - and trans -isomers of the polycyclic aromatic compound perinone, C 26 H 12 N 4 O 2 , form a solid solution (Vat Red 14). This is isotypic to crystal structures -perinone (Pigment 194) Orange 34) exhibits combined positional orientational disorder: In crystal, each molecular position occupied by either or molecule, both which have two possible orientations. structure twofold disorder, whereas ordered. was determined single-crystal X-ray analysis. Extensive lattice-energy...
Despite being the earliest reported case of polymorphism in a molecular crystal, unstable form II benzamide has thus far evaded thorough structural characterization because collection experimental data at atomic resolution proven extremely challenging. Using highly validated computational crystal structure prediction (CSP) method based on dispersion-corrected density functional theory, we correctly predict stable I with lowest energy among all sampled structures and its polytypic III...