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1. 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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2. Dockground scoring benchmarks for protein docking

   https://doi.org/10.1002/prot.26306  

   Kotthoff, Ian; Kundrotas, Petras J.; Vakser, Ilya A. (June 2022, Proteins: Structure, Function, and Bioinformatics)
3. MucR protein: Three decades of studies have led to the identification of a new H‐NS ‐like protein

   https://doi.org/10.1111/mmi.15261  

   Baglivo, Ilaria; Malgieri, Gaetano; Roop, II, Roy_Martin; Barton, Ian_S; Wang, Xindan; Russo, Veronica; Pirone, Luciano; Pedone, Emilia_M; Pedone, Paolo_V (April 2024, Molecular Microbiology)

   Abstract MucR belongs to a large protein family whose members regulate the expression of virulence and symbiosis genes in α‐proteobacteria species. This protein and its homologs were initially studied as classical transcriptional regulators mostly involved in repression of target genes by binding their promoters. Very recent studies have led to the classification of MucR as a new type of Histone‐like Nucleoid Structuring (H‐NS) protein. Thus this review is an effort to put together a complete and unifying story demonstrating how genetic and biochemical findings on MucR suggested that this protein is not a classical transcriptional regulator, but functions as a novel type of H‐NS‐like protein, which binds AT‐rich regions of genomic DNA and regulates gene expression. 

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4. HAIRY MERISTEM proteins regulate the WUSCHEL protein levels in mediating CLAVATA3 expression

   https://doi.org/10.1111/ppl.14505  

   Rodriguez, Kevin; Kao, Lloyd; Cerbantez‐Bueno, Vincent_E; Delgadillo, Christian; Nguyen, Dorothy; Ullah, Samin; Delgadillo, Cameron; Reddy, G_Venugopala (September 2024, Physiologia Plantarum)

   Abstract The precise regulation of stem cells in the shoot apical meristems (SAMs) involves the function of the homeodomain transcription factor (TF)‐WUSCHEL (WUS). WUS has been shown to move from the site of production‐the rib‐meristem (RM), into overlaying cells of the central zone (CZ), where it specifies stem cells and also regulates the transcription ofCLAVATA3 (CLV3). The secreted signalling peptide CLV3 activates a receptor kinase signalling that restrictsWUStranscription and also regulates the nuclear gradient of WUS by offsetting nuclear export. WUS has been shown to regulate bothCLV3levels and spatial activation, restricting its expression to a few cells in the CZ. The HAIRY MERISTEM (HAM), a GRASS‐domain class of TFs expressed in the RM, has been shown to physically interact with WUS and regulateCLV3expression. However, the mechanisms by which this interaction regulatesCLV3expression non‐cell autonomously remain unclear. Here, we show that HAM function is required for regulating the WUS protein stability, and theCLV3expression responds to altered WUS protein levels inhammutants. Thus, HAM proteins non‐cell autonomously regulatesCLV3expression. 

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5. Accurate ligand–protein docking in CASP15 using the ClusPro LigTBM server

   https://doi.org/10.1002/prot.26587  

   Kotelnikov, Sergei; Ashizawa, Ryota; Popov, Konstantin_I; Khan, Omeir; Ignatov, Mikhail; Li, Stan_Xiaogang; Hassan, Mosavverul; Coutsias, Evangelos_A; Poda, Gennady; Padhorny, Dzmitry; et al (September 2023, Proteins: Structure, Function, and Bioinformatics)

   Abstract In the ligand prediction category of CASP15, the challenge was to predict the positions and conformations of small molecules binding to proteins that were provided as amino acid sequences or as models generated by the AlphaFold2 program. For most targets, we used our template‐based ligand docking program ClusPro ligTBM, also implemented as a public server available athttps://ligtbm.cluspro.org/. Since many targets had multiple chains and a number of ligands, several templates, and some manual interventions were required. In a few cases, no templates were found, and we had to use direct docking using the Glide program. Nevertheless, ligTBM was shown to be a very useful tool, and by any ranking criteria, our group was ranked among the top five best‐performing teams. In fact, all the best groups used template‐based docking methods. Thus, it appears that the AlphaFold2‐generated models, despite the high accuracy of the predicted backbone, have local differences from the x‐ray structure that make the use of direct docking methods more challenging. The results of CASP15 confirm that this limitation can be frequently overcome by homology‐based docking. 

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