Topic 129

biochemistry enzymes enzyme substrate amino acid acids proteins catalytic protein substrates enzymatic reactions chemical reaction coli biosynthesis peptide modification synthetic biosynthetic synthesis report peptides fold affinity applications engineering natural purified recombinant sequence products structure active discovery catalyze activity residues product residue produced site specificity escherichia native biochemical structural screening cysteine encoded synthetase translational purification modified binding step synthase stability cofactor bonds activities synthesized kinetic vitro heterologous terminal properties tags compounds engineered modifications probes ribosomally non hydrogen hydrolysis kd folding reported assays degradation covalently first libraries molecules characterization precursor produce cyclic class uncharacterized family directed form catalyzed beta synthases cleavage nucleic

291 items. Top items listed below.

Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia 129 63 8

Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases 129 63 8 4

Design of optical imaging probes by screening of diverse substrate libraries directly in disease tissue extracts 129 18 14 4

Modulation of plant Acetyl CoA Synthetase activity by acetylation 199 129 63 16 8 3

Evolution-based design of chorismate mutase enzymes 129 63 8

Mechanism-based enzyme activating compounds 63 8

A bead-based method for the removal of the amino acid lysine from cell-free transcription-translation systems 129 8

Single amino acid-promoted reactions link a non-enzymatic chemical network to the early evolution of enzymatic pentose phosphate pathway 129 67 63 8

RRE-Finder: A Genome-Mining Tool for Class-Independent RiPP Discovery 129 4

Phase Separation Can Increase Enzyme Activity by Concentration and Molecular Organization 129 78 8

Promiscuous enzymes cooperate at the substrate level en route to lactazole A 129 8

In vivo selection for formate dehydrogenases with high efficiency and specificity towards NADP+ 129 67 63 8

Quantifying Evolutionary Importance of Protein Sites: A Tale of Two Measures 129 8

The evolution of human SIRT1 for multi-specificity is enabled by active-site adaptation 63 8

Exploring the conformational landscape of a lanthipeptide synthetase using native mass spectrometry 129 63 45 8

A general in vitro assay to study enzymatic activities of the ubiquitin system 129 63 8

System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA) 129 63 8

Engineered unnatural ubiquitin for optimal detection of deubiquitinating enzymes 196 129 63 8

Structure of SARS-CoV-2 main protease in the apo state reveals the inactive conformation 44 1

Isolation of Chemically Cyclized Peptide Binders Using Yeast Surface Display 129 8

A highly diverged ancient interface plays a key role in the origin and evolution of Methionine AdenosylTransferase superfamily 40 8 5

Directed evolution of Anabaena variabilis phenylalanine ammonia-lyase (PAL) identifies mutants with enhanced activities 129 63 33

Rapid in vitro prototyping of O-methyltransferases for pathway applications in Escherichia coli 129 67 12

Influence of spatial structure on protein damage susceptibility - A bioinformatics approach 129 8

Computational genomic discovery of diverse gene clusters harboring Fe-S flavoenzymes in anaerobic gut microbiota 143 29 12 5

The E. coli NudL enzyme is a Nudix hydrolase that cleaves CoA and its derivatives 129 63 8

Exploring the selenium-over-sulfur substrate specificity and kinetics of a bacterial selenocysteine lyase 129 63 8 3

Substrate specificity profiling of SARS-CoV-2 main protease enables design of activity-based probes for patient-sample imaging 44 1

Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition interface 49 31 8 3

Efficient rational modification of non-ribosomal peptides by adenylation domain substitution 129 63 8

Updates on enzymatic and structural properties of human glutamine: fructose-6-phosphate amidotransferase 2 (hGFAT2) 178 63 8

Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates 136 49 8

Exploring Potential Signals of Selection for Disordered Residues in Naturally Occurring Prokaryotic and Eukaryotic Proteins 149 8

Towards XNA molecular biology: Bacterial cell display as a robust and versatile platform for the engineering of low affinity ligands and enzymes 129 33 18 8

The proteasome-related Connectase is a fast and specific protein ligase 129 63 8

Insights into the catalytic properties of the mitochondrial rhomboid protease PARL 129 63 8

Global chemical modifications comparison of human plasma proteomes from two different age groups 45 15 8

Protein covariance networks reveal interactions important to the emergence of SARS coronaviruses as human pathogens 37 1

Engineering protein-specific proteases: targeting active RAS 63 8 3

The relationship between effective molarity and affinity governs rate enhancements in tethered kinase-substrate reactions 129 8

Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling 38 4

Optimizing model comparison for enzymatic mechanism analysis 129 63 8

The electrostatic allostery could be the trigger for the changes in dynamics for the PDZ domain of PICK1 63 8 3

Epistasis on the stability landscape of de novo TIM barrels explored by a modular design approach 129 63 8

Evolution of structural dynamics in bilobed proteins 63 8 3

A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data 38 8

Analysis of Metabolic Network Disruption in Engineered Microbial Hosts due to Enzyme Promiscuity 67 38 33 12

Synthesis and Evaluation of a Stable Isostere of Malonyllysine 129 67 63

Ebselen as a highly active inhibitor of PLProCoV2 44 1

Breaking a Strong Amide Bond: Structure and Properties of Dimethylformamidase. 63 8

Ubiquitin Substrates Dramatically Increase Ataxin3 Deubiquitinating Activity: Allosteric crosstalk connects three distinct sites 63 8 3

Real-time structural motif searching in proteins using an inverted index strategy 140 4

Enzymatic RNA Biotinylation for Affinity Purification and Identification of RNA-protein Interactions 196 151 45 8 3

Discovery of 20 novel ribosomal leaders in bacteria and archaea 49 31 8

Deep learning enables the design of functional de novo antimicrobial proteins 105 26 4

Molecular Basis for ADP-ribose Binding to the Macro-X Domain of SARS-CoV-2 Nsp3 1

Cheminformatics Analysis of Natural Product Scaffolds: Comparison of Scaffolds Produced by Animals, Plants, Fungi and Bacteria 129 4

The C-terminus is critical for the degradation of substrates by the Pseudomonas aeruginosa CtpA protease 79 8 3

CRISPR-Cas9-mediated depletion of O-GlcNAc hydrolase and transferase for functional dissection of O-GlcNAcylation in human cells 33 3

Perturbing proteomes at single residue resolution using base editing 139 33 9 4

Machine Learning and Optimal Control of Enzyme Activities to Preserve Solvent Capacity in the Cell 67 38 26 4

A Legionella effector kinase is activated by host inositol hexakisphosphate 63 8 3

Exploring the Sequence Fitness Landscape of a Bridge Between Protein Folds 149 91 38 8 4

Engineering a virus-like particle to display peptide insertions using an apparent fitness landscape 129 8

Peptide-based Inhibitors of Protein-Protein Interactions of Src Homology 2 Domain-Containing Phosphatase 2 102 63 3

Chemical modification of proteins by insertion of synthetic peptides using tandem protein trans-splicing 198 129 18 8

An atlas of Arabidopsis protein S-Acylation reveals its widespread role in plant cell organisation of and function. 16 8

Algal Neurotoxin Biosynthesis Repurposes the Terpene Cyclase Structural Fold Into an N-prenyltransferase 199 129 63 8

A second hybrid-binding domain modulates the activity of Drosophila ribonuclease H1 63 8 3

Naturally occurring cobalamin (B12) analogs can function as cofactors for human methylmalonyl-CoA mutase 129 63

Learning Peptide Recognition Rules for a Low-Specificity Protein 63 8 4

Stimulation of the human mitochondrial transporter ABCB10 by zinc-mesoporphrin 95 63 8 3

Extension of a de novo TIM barrel with a rationally designed secondary structure element 63 8 4

Peptide recognition and dephosphorylation by the vaccinia VH1 phosphatase 63 8 3

Structural basis for the recognition of the 2019-nCoV by human ACE2 36 1

An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity 63 8 3

Comparative analysis of CPI-motif regulation of biochemical functions of actin capping protein 63 8

Expanding the chemical space of synthetic cyclic peptides using a promiscuous macrocyclase from prenylagaramide biosynthesis 129 63 8

Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology 31 8

sPepFinder expedites genome-wide identification of small proteins in bacteria 105 26 4

An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism 129 63 16 8 3

A dual-reporter system for investigating and optimizing protein translation and folding in E. coli 129 18 8 4

Recapitulating the frataxin activation mechanism in an engineered bacterial cysteine desulfurase supports the architectural switch model 63 8 3

Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors 44 1

The SARS-CoV-2 conserved macrodomain is a highly efficient ADP-ribosylhydrolase 1

Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses 129 121 8

On-rate modulation of cadherin interactions by chemical fragments 151 63 8 3

The role of anionic amino acids in hydrolysis of poly-β-(1,6)-N-acetylglucosamine exopolysaccharides by the biofilm dispersing glycosidase Dispersin B 63 8 3

Harnessing Ionic Selectivity In Acetyltransferase Chemoproteomic Probes 129 63 18 8

Systematic Engineering of Artificial Metalloenzymes for New-to-Nature Reactions 129 33 18

Raman spectroscopy-based measurements of single-cell phenotypic diversity in microbial communities 158 38 18 17 5

Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria 129 63 12 8

Identification of ubiquitin Ser57 kinases regulating the oxidative stress response in yeast 102 34 3

A cooperative network of molecular "hot spots" highlights the complexity of LH3 collagen glycosyltransferase activities 63 8

Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases 105 26 4

Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design 44 1

Structural and Dynamic Basis of Molecular Recognition between Acyltransferase and Carrier Protein in E. coli Fatty Acid Synthesis 63 8 3

Global impact of phosphorylation on protein endurance 45 18 4

N-glucosyltransferase GbNGT1 from Ginkgo complement auxin metabolic pathway 129 63 16

Actin-binding compounds, discovered by FRET-based high-throughput screening, differentially affect skeletal and cardiac muscle 55 8