Paul D. Adams
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View article: Enzymology and Structural Basis of Glycosyltransferases Involved in Saponin C28 Carboxylic Acid <i>O</i> - <scp>d</scp> -Fucosylation
Enzymology and Structural Basis of Glycosyltransferases Involved in Saponin C28 Carboxylic Acid <i>O</i> - <span>d</span> -Fucosylation Open
View article: One-step purification of a bioactive PAK1-derived peptide
One-step purification of a bioactive PAK1-derived peptide Open
The serine/threonine kinase PAK1 serves as a mediator of cytoskeletal reorganization and cancer-related signaling downstream of the small GTPases. Due to the challenges in purifying PAK1 complexes, a 46-residue peptide from PAK1, is widely…
View article: Predictive CRISPR-mediated gene downregulation for enhanced production of sustainable aviation fuel precursor in Pseudomonas putida
Predictive CRISPR-mediated gene downregulation for enhanced production of sustainable aviation fuel precursor in Pseudomonas putida Open
CRISPR interference (CRISPRi) has emerged as a valuable tool for redirecting metabolic flux to enhance bioproduction. However, its application is often constrained by two challenges: (i) rationally identifying effective gene targets for do…
View article: Diversity-driven biochemical survey reveals dimeric structural origin of rubisco
Diversity-driven biochemical survey reveals dimeric structural origin of rubisco Open
Rubisco is the entry point of nearly all organic carbon into the biosphere and is present in all domains of life. Despite its global importance, biochemical studies of this enzyme superfamily have been limited to a relatively narrow set of…
View article: Biosensor-driven strain engineering reveals key cellular processes for maximizing isoprenol production in <i>Pseudomonas putida</i>
Biosensor-driven strain engineering reveals key cellular processes for maximizing isoprenol production in <i>Pseudomonas putida</i> Open
Synthetic biology generates vast combinatorial designs, yet high-throughput analytical methods to screen them are poorly matched to interrogate this search space. We address this challenge by developing a biosensor-driven, growth-coupled s…
View article: AQuaRef: machine learning accelerated quantum refinement of protein structures
AQuaRef: machine learning accelerated quantum refinement of protein structures Open
View article: A large-scale screening campaign of putative carbohydrate-active enzymes reveals a novel xylanase from anaerobic gut fungi
A large-scale screening campaign of putative carbohydrate-active enzymes reveals a novel xylanase from anaerobic gut fungi Open
The genomes of anaerobic gut fungi (AGF) encode a diverse array of carbohydrate-active enzymes (CAZymes), yet exceedingly few of these enzymes have been experimentally validated or expressed in heterologous systems. Here, we developed a pr…
View article: Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields
Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields Open
In macromolecular structure refinement the low observation-to-parameter ratio and the lack of high-resolution data is countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in…
View article: High-Throughput Microfluidic Electroporation (HTME): A Scalable, 384-Well Platform for Multiplexed Cell Engineering
High-Throughput Microfluidic Electroporation (HTME): A Scalable, 384-Well Platform for Multiplexed Cell Engineering Open
Electroporation-mediated gene delivery is a cornerstone of synthetic biology, offering several advantages over other methods: higher efficiencies, broader applicability, and simpler sample preparation. Yet, electroporation protocols are of…
View article: Biochemical and structural characterization of glycosyltransferase family 61 proteins reveal a key determinant of sugar donor specificity
Biochemical and structural characterization of glycosyltransferase family 61 proteins reveal a key determinant of sugar donor specificity Open
Xylan, the most abundant non-cellulosic polymer in plant cell walls, is structurally diverse, especially in grasses where it is heavily substituted with arabinofuranose and further modified by various residues. Common substitutions across …
View article: Automation and machine learning drive rapid optimization of isoprenol production in Pseudomonas putida
Automation and machine learning drive rapid optimization of isoprenol production in Pseudomonas putida Open
Advances in genome engineering have improved our ability to perturb microbial metabolic networks, yet bioproduction campaigns often struggle with parsing complex metabolic datasets to efficiently enhance product titers. We address this cha…
View article: ALS-ENABLE: creating synergy and opportunity at the Advanced Light Source synchrotron structural biology beamlines
ALS-ENABLE: creating synergy and opportunity at the Advanced Light Source synchrotron structural biology beamlines Open
ALS-ENABLE is an integrated NIH P30 resource at the Advanced Light Source synchrotron at Lawrence Berkeley National Laboratory in Berkeley, California, USA. The resource provides a single portal to the combined mature structural biology te…
View article: Author Correction: Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida
Author Correction: Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida Open
View article: Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer
Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer Open
View article: Predictive genome-wide CRISPR-mediated gene downregulation for enhanced bioproduction
Predictive genome-wide CRISPR-mediated gene downregulation for enhanced bioproduction Open
CRISPR interference (CRISPRi) has emerged as a valuable tool for redirecting metabolic flux to enhance bioproduction. However, conventional approaches for identifying target genes for CRISPRi-mediated downregulation have largely relied on …
View article: Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida
Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida Open
Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obt…
View article: Enzymatic cleavage of model lignin dimers depends on pH, enzyme, and bond type
Enzymatic cleavage of model lignin dimers depends on pH, enzyme, and bond type Open
Lignin is composed of phenylpropanoid monomers linked by ether and carbon-carbon bonds to form a complex heterogeneous structure. Bond-specific studies of lignin-modifying enzymes (LMEs; e.g., laccases and peroxidases) are limited by the p…
View article: Biosensor-Driven Strain Engineering Reveals Key Cellular Processes for Maximizing Isoprenol Production in <i>Pseudomonas putida</i>
Biosensor-Driven Strain Engineering Reveals Key Cellular Processes for Maximizing Isoprenol Production in <i>Pseudomonas putida</i> Open
Synthetic biology tools have accelerated the generation of simple mutants, but combinatorial testing remains challenging. High-throughput methods struggle translating from proof-of-principle molecules to advanced bioproducts. We address th…
View article: A computational-guided framework and versatile assembly method for genome-wide CRISPRi downregulation in metabolic engineering studies
A computational-guided framework and versatile assembly method for genome-wide CRISPRi downregulation in metabolic engineering studies Open
View article: Using the Quantum Interface in Phenix to improve macromolecular model and ligand structures
Using the Quantum Interface in Phenix to improve macromolecular model and ligand structures Open
Quantum Mechanical methods provide geometries and energies of molecules using just the atomic and electronic positions. Being independent of the experimental data, they provide complementary information. Furthermore, allowing the experimen…
View article: A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxy acids
A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxy acids Open
View article: A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxyacids
A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxyacids Open
Medium- and branched-chain diols and amino alcohols are important industrial solvents, polymer building blocks, cosmetics and pharmaceutical ingredients, yet biosynthetically challenging to produce. Here, we present a novel approach utilis…
View article: The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity
The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity Open
View article: EcoFAB 3.0: a sterile system for studying sorghum that replicates previous field and greenhouse observations
EcoFAB 3.0: a sterile system for studying sorghum that replicates previous field and greenhouse observations Open
Introduction Studying plant-microbe interactions is one of the key elements in understanding the path to sustainable agricultural practices. These interactions play a crucial role in ensuring survival of healthy plants, soil and microbial …
View article: Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida
Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida Open
Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obt…
View article: Characterization of lignin-degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid
Characterization of lignin-degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid Open
Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS) dehydro…
View article: Protonation of histidine rings using quantum-mechanical methods
Protonation of histidine rings using quantum-mechanical methods Open
Histidine can be protonated on either or both of the two N atoms of the imidazole moiety. Each of the three possible forms occurs as a result of the stereochemical environment of the histidine side chain. In an atomic model, comparing the …
View article: Structural and biochemical basis for regiospecificity of the flavonoid glycosyltransferase UGT95A1
Structural and biochemical basis for regiospecificity of the flavonoid glycosyltransferase UGT95A1 Open
Glycosylation is a predominant strategy plants use to fine-tune the properties of small molecule metabolites to affect their bioactivity, transport, and storage. It is also important in biotechnology and medicine as many glycosides are uti…
View article: Likelihood-based interactive local docking into cryo-EM maps in <i>ChimeraX</i>
Likelihood-based interactive local docking into cryo-EM maps in <i>ChimeraX</i> Open
The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map…
View article: AQuaRef: Machine learning accelerated quantum refinement of protein structures
AQuaRef: Machine learning accelerated quantum refinement of protein structures Open
Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical restraints, which, in addition to being limited to kn…