A5061653192- Enzyme Structure and Function
- Biochemical and Molecular Research
- Protein Structure and Dynamics
- Biofuel production and bioconversion
- Microbial Natural Products and Biosynthesis
- Enzyme Production and Characterization
- Microbial Metabolic Engineering and Bioproduction
- Enzyme Catalysis and Immobilization
- Heat shock proteins research
- RNA and protein synthesis mechanisms
- Plant biochemistry and biosynthesis
- Amino Acid Enzymes and Metabolism
- Glycosylation and Glycoproteins Research
- Soil and Unsaturated Flow
- Landslides and related hazards
- Cytomegalovirus and herpesvirus research
- Fungal Biology and Applications
- Bacteriophages and microbial interactions
- Polysaccharides and Plant Cell Walls
- Photosynthetic Processes and Mechanisms
- HIV/AIDS drug development and treatment
- Geotechnical Engineering and Soil Stabilization
- Polyamine Metabolism and Applications
- Grouting, Rheology, and Soil Mechanics
- Microbial Metabolites in Food Biotechnology
Joint BioEnergy Institute
2015-2024
Lawrence Berkeley National Laboratory
2015-2024
Elucid Bioimaging
2020
Solvay (Brazil)
2017
University of California, Berkeley
2008-2009
Universidade Estadual Paulista (Unesp)
2000-2008
Centro Universitário de Rio Preto
2004-2008
Universidade de Brasília
1998-2005
University of Saskatchewan
2000-2005
Instituto Butantan
2003
Deep learning takes on protein folding In 1972, Anfinsen won a Nobel prize for demonstrating connection between protein’s amino acid sequence and its three-dimensional structure. Since 1994, scientists have competed in the biannual Critical Assessment of Structure Prediction (CASP) protein-folding challenge. methods took center stage at CASP14, with DeepMind’s Alphafold2 achieving remarkable accuracy. Baek et al . explored network architectures based DeepMind framework. They used three-track...
Building with designed proteins General design principles for protein interaction specificity are challenging to extract. DNA nanotechnology, on the other hand, has harnessed limited set of hydrogen-bonding interactions from Watson-Crick base-pairing and build a wide range shapes. Protein-based materials have potential even greater geometric chemical diversity, including additional functionality. Boyken et al. class oligomers that determined by modular arrays extensive hydrogen bond networks...
Designing proteins with cavities In de novo protein design, creating custom-tailored binding sites is a particular challenge because these often involve nonideal backbone structures. For example, curved b sheets are common ligand motif. Marcos et al. investigated the principles that drive β-sheet curvature by studying geometry of β in natural and folding simulations. step toward custom design enzyme catalysts, they used to control differently shaped cavities. Science , this issue p. 201
Lignin poses a major challenge in the processing of plant biomass for agro-industrial applications. For bioengineering purposes, there is pressing interest identifying and characterizing enzymes responsible biosynthesis lignin. Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase (HCT; EC 2.3.1.133) key metabolic entry point synthesis most important lignin monomers: coniferyl sinapyl alcohols. In this study, we investigated substrate promiscuity HCT from bryophyte ( Physcomitrella )...
The mechanical behavior of a compacted metastable-structured residual gneiss soil was experimentally investigated. Volume changes were investigated using both conventional oedometer cell and triaxial permeameter system where the stress state variables independently controlled. Wetting paths utilized to reflect field conditions associated with collapsing earth structures. specimens consolidated under isotropic k0-oedometer conditions. Measurements total volume change water content made at...
P. putida lysine metabolism can produce multiple commodity chemicals, conferring great biotechnological value. Despite much research, the connection of catabolism to central in remained undefined. Here, we used random barcode transposon sequencing fill gaps . We describe a route 2-oxoadipate (2OA) catabolism, which utilizes DUF1338-containing protein 5260 (PP_5260) bacteria. its prevalence many domains life, proteins have had no known biochemical function. demonstrate that PP_5260 is...
Significance NOV1 is a stilbene cleavage oxygenase (SCO). SCOs cleave the central double bond of stilbenes, forming two phenolic aldehydes. Many such as resveratrol, are produced by plants secondary metabolites. They also formed from lignin during kraft pulping. related to carotenoid oxygenases (CCOs), which β-carotene or apocarotenoids. Carotenoids play important roles in photosynthesis and light perception eye. We present structure an SCO CCO-related enzyme ternary complex with oxygen...
Chaperonins are large protein complexes consisting of two stacked multisubunit rings, which open and close in an ATP-dependent manner to create a protected environment for folding. Here, we describe the first crystal structure group II chaperonin conformation. We have obtained structures archaeal from Methanococcus maripaludis both peptide acceptor (open) state folding (closed) state. In contrast with I chaperonins, equatorial domains share similar conformation between closed states largest...
Significance This article reports the computational design of a threefold symmetric, self-assembling protein homotrimer containing highly stable noncanonical amino acid-mediated metal complex within interface. To achieve this result, recently developed protein–protein interface methods were extended to include metal-chelating acid bipyridine functional group in process. Bipyridine complexes can give rise photochemical properties that would be impossible with naturally occurring acids alone,...
Abstract Tightly regulated promoters are essential for numerous biological applications, where strong inducibility, portability, and scalability desirable. Current systems often incompatible with large-scale fermentations due to high inducer costs strict media requirements. Here, we describe the bottom-up engineering of ‘Jungle Express’, an expression system that enables efficient gene regulation in diverse proteobacteria. This is guided by EilR, a multidrug-binding repressor affinity its...
Abstract DeepMind presented remarkably accurate protein structure predictions at the CASP14 conference. We explored network architectures incorporating related ideas and obtained best performance with a 3-track in which information 1D sequence level, 2D distance map 3D coordinate level is successively transformed integrated. The produces accuracies approaching those of CASP14, enables rapid solution challenging X-ray crystallography cryo-EM modeling problems, provides insights into functions...
Major efforts in bioenergy research have focused on producing fuels that can directly replace petroleum-derived gasoline and diesel fuel through metabolic engineering of microbial fatty acid biosynthetic pathways. Typically, growth pathway induction are conducted under aerobic conditions, but for operational efficiency an industrial context, anaerobic culture conditions would be preferred to obviate the need maintain specific dissolved oxygen concentrations maximize proportion reducing...
There has been great progress in the development of technology for conversion lignocellulosic biomass to sugars and subsequent fermentation fuels. However, plant lignin remains an untapped source materials production fuels or high value chemicals. Biological cleavage well characterized fungi, which enzymes that create free radical intermediates are used degrade this material. In contrast, a catabolic pathway stereospecific β-aryl ether units found identified Sphingobium sp. SYK-6 bacteria....