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1. Substrates (Acyl‐ CoA and Diacylglycerol) Entry and Products ( CoA and Triacylglycerol) Egress Pathways in DGAT1

   https://doi.org/10.1002/jcc.70108  

   Lee, Hwayoung; Im, Wonpil (April 2025, Journal of Computational Chemistry)

   ABSTRACT Diacylglycerol O‐acyltransferase 1 (DGAT1) is an integral membrane protein that uses acyl‐coenzyme A (acyl‐CoA) and diacylglycerol (DAG) to catalyze the formation of triacylglycerides (TAGs). The acyl transfer reaction occurs between the activated carboxylate group of the fatty acid and the free hydroxyl group on the glycerol backbone of DAG. However, how the two substrates enter DGAT1's catalytic reaction chamber and interact with DGAT1 remains elusive. This study aims to explore the structural basis of DGAT1's substrate recognition by investigating each substrate's pathway to the reaction chamber. Using a human DGAT1 cryo‐EM structure in complex with an oleoyl‐CoA substrate, we designed two different all‐atom molecular dynamics (MD) simulation systems: DGAT1^away(both acyl‐CoA and DAG away from the reaction chamber) and DGAT1^bound(acyl‐CoA bound in and DAG away from the reaction chamber). Our DGAT1^awaysimulations reveal that acyl‐CoA approaches the reaction chamber via interactions with positively charged residues in transmembrane helix 7. DGAT1^boundsimulations show DAGs entering into the reaction chamber from the cytosol leaflet. The bound acyl‐CoA's fatty acid lines up with the headgroup of DAG, which appears to be competent to TAG formation. We then converted them into TAG and coenzyme (CoA) and used adaptive biasing force (ABF) simulations to explore the egress pathways of the products. We identify their escape routes, which are aligned with their respective entry pathways. Visualization of the substrate and product pathways and their interactions with DGAT1 is expected to guide future experimental design to better understand DGAT1 structure and function. 

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2. Evolution of the SARS‐CoV ‐2 proteome in three dimensions (3D) during the first 6 months of the COVID ‐19 pandemic

   https://doi.org/10.1002/prot.26250  

   Lubin, Joseph H.; Zardecki, Christine; Dolan, Elliott M.; Lu, Changpeng; Shen, Zhuofan; Dutta, Shuchismita; Westbrook, John D.; Hudson, Brian P.; Goodsell, David S.; Williams, Jonathan K.; et al (October 2021, Proteins: Structure, Function, and Bioinformatics)

   Abstract Understanding the molecular evolution of the SARS‐CoV‐2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three‐dimensional structures of SARS‐CoV‐2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID‐19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein–protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi‐Gaussian distribution. Detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein–protein and protein–nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure‐based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance. 

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3. Functionalizing DNA nanostructures for therapeutic applications

   https://doi.org/10.1002/wnan.1729  

   Henry, Skylar J. W.; Stephanopoulos, Nicholas (May 2021, WIREs Nanomedicine and Nanobiotechnology)

   Abstract Recent advances in nanotechnology have enabled rapid progress in many areas of biomedical research, including drug delivery, targeted therapies, imaging, and sensing. The emerging field of DNA nanotechnology, in which oligonucleotides are designed to self‐assemble into programmable 2D and 3D nanostructures, offers great promise for further advancements in biomedicine. DNA nanostructures present highly addressable and functionally diverse platforms for biological applications due to their ease of construction, controllable architecture and size/shape, and multiple avenues for chemical modification. Both supramolecular and covalent modification with small molecules and polymers have been shown to expand or enhance the functions of DNA nanostructures in biological contexts. These alterations include the addition of small molecule, protein, or nucleic acid moieties that enable structural stability under physiological conditions, more efficient cellular uptake and targeting, delivery of various molecular cargos, stimulus‐responsive behaviors, or modulation of a host immune response. Herein, various types of DNA nanostructure modifications and their functional consequences are examined, followed by a brief discussion of the future opportunities for functionalized DNA nanostructures as well as the barriers that must be overcome before their translational use. This article is categorized under:Nanotechnology Approaches to Biology > Nanoscale Systems in BiologyTherapeutic Approaches and Drug Discovery > Emerging TechnologiesBiology‐Inspired Nanomaterials > Nucleic Acid‐Based Structures 

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4. Predicting protein flexibility with AlphaFold

   https://doi.org/10.1002/prot.26471  

   Ma, Puyi; Li, Da‐Wei; Brüschweiler, Rafael (February 2023, Proteins: Structure, Function, and Bioinformatics)

   Abstract AlphaFold2 has revolutionized protein structure prediction from amino‐acid sequence. In addition to protein structures, high‐resolution dynamics information about various protein regions is important for understanding protein function. Although AlphaFold2 has neither been designed nor trained to predict protein dynamics, it is shown here how the information returned by AlphaFold2 can be used to predict dynamic protein regions at the individual residue level. The approach, which is termed cdsAF2, uses the 3D protein structure returned by AlphaFold2 to predict backbone NMR NHS²order parameters using a local contact model that takes into account the contacts made by each peptide plane along the backbone with its environment. By combining for each residue AlphaFold2's pLDDT confidence score for the structure prediction accuracy with the predictedS²value using the local contact model, an estimator is obtained that semi‐quantitatively captures many of the dynamics features observed in experimental backbone NMR NHS²order parameter profiles. The method is demonstrated for a set nine proteins of different sizes and variable amounts of dynamics and disorder. 

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5. Composites produced from waste plastic with agricultural and energy sector by‐products

   https://doi.org/10.1002/app.54828  

   Lopez, Claudia V.; Smith, Rhett C. (November 2023, Journal of Applied Polymer Science)

   Abstract A three‐stage route to chemically upcycle post‐consumer poly(ethylene terephthalate) (PET) to produce high compressive strength composites is reported. This procedure involves initial glycolysis with diethylene glycol to produce a mixture (GPET) comprising oligomers of 2–7 terephthalate units followed by trans/esterification of GPET with fatty acid chains supplied by brown grease, an agricultural by‐product of animal fat of relatively low nutritional or fuel value. This process yields PGB comprising a mixture of mono‐terephthalate ester derivatives. The olefin units provided by unsaturated fatty acid chains in brown grease were crosslinked by an inverse vulcanization reaction with elemental sulfur to give composites GBS_x(x = wt% S, varied from 80%–90%). The compressive strengths of GBS₈₀(27.5 ± 2.6 MPa) and GBS₉₀(19.2 ± 0.8 MPa) exceed the compressive strength required of ordinary Portland cement (17 MPa) for its use in residential building foundations. The current route represents a way to repurpose waste plastic, energy sector by‐product sulfur, and agricultural by‐product brown grease to give high strength composites with mechanical properties suggesting their possible use to replace less sustainably sourced legacy structural materials. 

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