Structural analysis of protein tyrosine phosphatase 1B reveals potentially druggable allosteric binding sites by Kumar, Ammu Prasanna, Nguyen, Minh Nhan, Verma, Chandra, Lukman, Suryani

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Analysis of the role played by ligand-induced folding of the cocaine-binding aptamer in the photochrome aptamer switch assay by Shoara, Aron A., Churcher, Zachary R., Steele, Terry W. J., Johnson, Philip E.

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Alternative splicing in the DBD linker region of p63 modulates binding to DNA and iASPP in vitro by Lotz, R, Osterburg, C, Chaikuad, A, Weber, S, Akutsu, M, Machel, AC, Beyer, U, Gebel, J, Löhr, F, Knapp, S, Dobbelstein, M, Lu, X, Dötsch, V

“…Here we characterize the interaction of iASPP with p63 and show that it binds to the linker region between the DNA binding domain and the oligomerization domain. …”

Characterizing the conformational landscape of MDM2-binding p53 peptides using molecular dynamics simulations by Yadahalli, Shilpa, Li, Jianguo, Lane, David P., Gosavi, Shachi, Verma, Chandra Shekhar

“…The conformational landscapes of p53 peptide variants and phage derived peptide (12/1) variants, all known to bind to MDM2, are studied using hamiltonian replica exchange molecular dynamics simulations. …”
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Multiscale topological indices for the quantitative prediction of SARS CoV-2 binding affinity change upon mutations by Bi, Jialin, Wee, JunJie, Liu, Xiang, Qu, Cunquan, Wang, Guanghui, Xia, Kelin

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Regulation of mRNA abundance by polypyrimidine tract-binding protein-controlled alternate 5′ splice site choice by Hamid, Fursham M., Makeyev, Eugene V.

“…Here we report that polypyrimidine tract-binding protein 1 (Ptbp1/PTB/hnRNP-I) controls alternate 5′ and 3′ splice site (5′ss and 3′ss) usage in a large set of mammalian transcripts. …”
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Impact of molecular linker size on physicochemical properties of assembled gold nanoparticle mono-/multi-layers and their applicability for functional binding of biomolecules by Krikstolaityte, Vida, Hamit-Eminovski, Jildiz, Abariute, Laura, Niaura, Gediminas, Meskys, Rolandas, Arnebrant, Thomas, Lisak, Grzegorz, Ruzgas, Tautgirdas

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Linking dual mode of action of host defense antimicrobial peptide thanatin: structures, lipopolysaccharide and LptAm binding of designed analogs by Sinha, Sheetal, Dhanabal, Vidhya Bharathi, Sperandeo, Paola, Polissi, Alessandra, Bhattacharjya, Surajit

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Curvature sensing amphipathic helix in the C-terminus of RTNLB13 is conserved in all endoplasmic reticulum shaping reticulons in Arabidopsis thaliana by Brooks, Rhiannon L., Mistry, Chandni S., Dixon, Ann M.

“…The reticulon family of integral membrane proteins are conserved across all eukaryotes and typically localize to the endoplasmic reticulum (ER), where they are involved in generating highly-curved tubules. …”
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A conserved arginine in NS5 binds genomic 3' stem-loop RNA for primer-independent initiation of flavivirus RNA replication by Wang, Sai, Chan, Kitti Wing Ki, Tan, Min Jie Alvin, Flory, Charlotte, Luo, Dahai, Lescar, Julian, Forwood, Jade K., Vasudevan, Subhash G.

“…We show that DENV2 NS5 arginine 888, located within the carboxy-terminal 18 residues, is completely conserved in all flaviviruses and interacts specifically with the top-loop of 3'SL in the 3'UTR which contains the pentanucleotide 5'-CACAG-3' previously shown to be critical for flavivirus RNA replication. …”
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The binding interface of kindlin-2 and ILK involves Asp344/Asp352/Thr356 in kindlin-2 and Arg243/Arg334 in ILK by Tan, Hui-Foon, Guan, Si-Yu, Chng, Choon-Peng, Ong, Li-Teng, Tan, Suet-Mien, Law, Alex Sai Kit

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Sequence- and structure-specific probing of RNAs by short nucleobase-modified dsRNA-binding PNAs incorporating a fluorescent light-up uracil analog by Krishna, Manchugondanahalli Shivakumar, Toh, Desiree-Faye Kaixin, Meng, Zhenyu, Ong, Alan Ann Lerk, Wang, Zhenzhang, Lu, Yunpeng, Xia, Kelin, Prabakaran, Mookkan, Chen, Gang

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DNA-damage orchestrates self-renewal and differentiation via reciprocal p53 family and Hippo/Wnt/TGF-β pathway activation in embryonic stem cells by Ye, Y, Xie, W, Wang, X, Tan, S, Yang, L, Ma, Z, Zhu, Z, Chen, X, Liu, X, O’Neill, E, Chang, L, Zhang, W

“…Notably, our study reveals that irradiation-induced DNA damage leads to the recruitment of the BAF complex, causing it to dissociate from its binding sites on the target genes associated with the Yap, Wnt, and TGF-β pathways, thereby increasing signaling and promoting differentiation of ESCs into all three lineages. …”

Bond order resolved 3d 5/2 and valence band chemical shifts of Ag surfaces and nanoclusters by Sun, Changqing, Qin, Wei, Wang, Yan, Huang, Yongli, Zhou, Zhaofeng, Yang, Chao

“…Incorporating the tight-binding theory and the bond order–length–strength (BOLS) correlation into the X-ray photoelectron spectra of Ag(111) and (100) surfaces and the Auger electron spectra of Ag nanoparticles deposited on Al2O3 and CeO2 substrates has led to quantitative information of the 3d5/2 and the valence binding energies of an isolated Ag atom and their shifts upon bulk, defect, surface, and nanocrystal formation. …”
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Elucidating the mechanism of mRNA transport using novel imaging technologies by Stoychev, D

“…The MS2-MCP system is used to insert into mRNAs of interest special structures to which RNA-binding proteins, fused to a fluorescent protein such as GFP, can then bind. …”

Membrane reconstitution of monoamine oxidase enzymes on supported lipid bilayers by Wang, Liulin, Kabir H. Biswas, Yoon, Bo Kyeong, Kawakami, Lisa M., Park, Soohyun, Groves, Jay T., Li, Lin, Huang, Wei, Cho, Nam-Joon

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Unconventional split aptamers cleaved at functionally essential sites preserve biorecognition capability by Wang, Ruoyu, Zhang, Qiansen, Zhang, Yi, Shi, Hanchang, Nguyen, Kim Truc, Zhou, Xiaohong

“…An allosteric binding mechanism of BPSPAs, in which a new binding pocket is formed upon the target binding, is revealed by all-atom microsecond-scale molecular dynamics simulations. …”
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Part I Targeting RNA duplexes with modified triplex-forming oligonucleotides Part II Allostery within a Watson-Crick RNA duplex and its application in studying RNA recognition by R... by Zhou, Yuan

“…Here, we incorporated Locked Nucleic Acid (LNA), 2-thio U, and 2′-O methyl modified residues in a series of all pyrimidine RNA TFOs, and studied the binding to two RNA hairpin structures. 12-Base-triple major-groove pyrimidine•purine-pyrimidine triplex structures form between the RNA/DNA hairpins and the complementary RNA TFOs. …”
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Membrane cholesterol modulates oligomeric status and peptide-membrane interaction of severe acute respiratory syndrome coronavirus fusion peptide by Meher, Geetanjali, Bhattacharjya, Surajit, Chakraborty, Hirak

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CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil by Almqvist, Helena, Axelsson, Hanna, Jafari, Rozbeh, Dan, Chen, Mateus, André, Haraldsson, Martin, Larsson, Andreas, Molina, Daniel Martinez, Artursson, Per, Lundbäck, Thomas, Nordlund, Pär

“…Assessment of compound binding to native target proteins in live cells is therefore highly desirable in all stages of drug discovery. …”
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