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Nienke Elizabeth van Houten - Related publications

2010- Health Sciences Simon Fraser University, Burnaby, British Columbia, Canada 
molecular immunology and vaccine design
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Pao PJ, Hsu MF, Chiang MH, Chen CT, Lee CC, Wang AH. Structural basis of an epitope tagging system derived from Haloarcula marismortui bacteriorhodopsin I D94N and its monoclonal antibody GD-26. The Febs Journal. PMID 34499806 DOI: 10.1111/febs.16184   
2021 Sun L, Fu T, Zhao D, Fan H, Zhong S. Divide-and-link peptide docking: a fragment-based peptide docking protocol. Physical Chemistry Chemical Physics : Pccp. PMID 34596658 DOI: 10.1039/d1cp02098f   
2021 McCaul N, Quandte M, Bontjer I, van Zadelhoff G, Land A, Crooks ET, Binley JM, Sanders RW, Braakman I. Intramolecular quality control: HIV-1 envelope gp160 signal-peptide cleavage as a functional folding checkpoint. Cell Reports. 36: 109646. PMID 34469718 DOI: 10.1016/j.celrep.2021.109646   
2021 Ascencio-Ibáñez JT, Bobay BG. Conserved Structural Motif Identified in Peptides That Bind to Geminivirus Replication Protein Rep. Biochemistry. PMID 34464102 DOI: 10.1021/acs.biochem.1c00408   
2021 Johnson RM, Zhang X, Piper SJ, Nettleton TJ, Vandekolk TH, Langmead CJ, Danev R, Sexton PM, Wootten D. Cryo-EM structure of the dual incretin receptor agonist, peptide-19, in complex with the glucagon-like peptide-1 receptor. Biochemical and Biophysical Research Communications. 578: 84-90. PMID 34547628 DOI: 10.1016/j.bbrc.2021.09.016   
2021 Lü Y, Bai J, Tan D, Chen T, Shan A. [The effects of hinge structure on the biological activity of antimicrobial peptides and its application in molecular design: a review]. Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. 37: 3142-3150. PMID 34622623 DOI: 10.13345/j.cjb.200728   
2021 Zhang D, Wu H, Zhao J. Computational design and experimental substantiation of conformationally constrained peptides from the complex interfaces of transcriptional enhanced associate domains with their cofactors in gastric cancer. Computational Biology and Chemistry. 94: 107569. PMID 34500324 DOI: 10.1016/j.compbiolchem.2021.107569   
2021 Tang R, Song Y, Shi M, Jiang Z, Zhang L, Xiao Y, Tian Y, Zhou S. Rational Design of a Dual-Targeting Natural Toxin-Like Bicyclic Peptide for Selective Bioenergetic Blockage in Cancer Cells. Bioconjugate Chemistry. PMID 34606715 DOI: 10.1021/acs.bioconjchem.1c00366   
2021 Unarta IC, Xu J, Shang Y, Cheung CHP, Zhu R, Chen X, Cao S, Cheung PP, Bierer D, Zhang M, Huang X, Li X. Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain. Rsc Chemical Biology. 2: 1274-1284. PMID 34458841 DOI: 10.1039/d1cb00087j   
2021 Efaz FM, Islam S, Talukder SA, Akter S, Tashrif MZ, Ali MA, Sufian MA, Parves MR, Islam MJ, Halim MA. Repurposing fusion inhibitor peptide against SARS-CoV-2. Journal of Computational Chemistry. PMID 34591335 DOI: 10.1002/jcc.26758   
2021 Liu Y, Shao X, Wang T, Wang X, Li N, Zhao Y, Xia W, Sun L. [Structure prediction and biological activity analysis of dybowskin-1ST antimicrobial peptide in Rana dybowskii]. Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology. 37: 2890-2902. PMID 34472306 DOI: 10.13345/j.cjb.200564   
2021 Zhou M, Wen H, Lei H, Zhang T. Molecular dynamics study of conformation transition from helix to sheet of Aβ42 peptide. Journal of Molecular Graphics & Modelling. 109: 108027. PMID 34534891 DOI: 10.1016/j.jmgm.2021.108027   
2021 Lee KH, Chang YC, Chen TF, Juan HF, Tsai HK, Chen CY. Connecting MHC-I-binding motifs with HLA alleles via deep learning. Communications Biology. 4: 1194. PMID 34663927 DOI: 10.1038/s42003-021-02716-8   
2021 Qin X, Chen H, Tu L, Ma Y, Liu N, Zhang H, Li D, Riedl B, Bierer D, Yin F, Li Z. Potent Inhibition of HIF1α and p300 Interaction by a Constrained Peptide Derived from CITED2. Journal of Medicinal Chemistry. PMID 34472840 DOI: 10.1021/acs.jmedchem.1c01043   
2021 Sanches K, Wai DCC, Norton RS. Conformational dynamics in peptide toxins: Implications for receptor interactions and molecular design. Toxicon : Official Journal of the International Society On Toxinology. 201: 127-140. PMID 34454969 DOI: 10.1016/j.toxicon.2021.08.020   
2021 Behzadipour Y, Gholampour M, Pirhadi S, Seradj H, Khoshneviszadeh M, Hemmati S. Viral 3CL as a Target for Antiviral Intervention Using Milk-Derived Bioactive Peptides. International Journal of Peptide Research and Therapeutics. 1-14. PMID 34548852 DOI: 10.1007/s10989-021-10284-y   
2021 Wang P, Yue C, Liu K, Lu D, Liu S, Yao S, Li X, Su X, Ren K, Chai Y, Qi J, Zhao Y, Lou Y, Sun Z, Gao GF, et al. Peptide Presentations of Marsupial MHC Class I Visualize Immune Features of Lower Mammals Paralleled with Bats. Journal of Immunology (Baltimore, Md. : 1950). PMID 34535575 DOI: 10.4049/jimmunol.2100350   
2021 Si W, Yang H, Wu G, Zhang Y, Sha J. Velocity control of protein translocation through a nanopore by tuning the fraction of benzenoid residues. Nanoscale. PMID 34498657 DOI: 10.1039/d1nr04492c   
2021 Honisch C, Ragazzi E, Hussain R, Brazier J, Siligardi G, Ruzza P. Interaction of a Short Peptide with G-Quadruplex-Forming Sequences: An SRCD and CD Study. Pharmaceutics. 13. PMID 34452065 DOI: 10.3390/pharmaceutics13081104   
2021 Saranya V, Shankar R, Gatasheh MK, Zehra S. Impact of Au metal clusters on the structural and inhibitory mechanism of Aβ peptide: A theoretical approach. Environmental Research. 204: 111920. PMID 34464618 DOI: 10.1016/j.envres.2021.111920   
2021 Dhusia K, Su Z, Wu Y. A structural-based machine learning method to classify binding affinities between TCR and peptide-MHC complexes. Molecular Immunology. 139: 76-86. PMID 34455212 DOI: 10.1016/j.molimm.2021.07.020   
2021 Faragó Z, Mirzahosseini A, Horváth D, Pálla T, Horváth P, Perczel A, Noszál B. Solution Structure and Acid-Base Properties of Reduced α-Conotoxin MI. Chemistry & Biodiversity. e2100464. PMID 34467647 DOI: 10.1002/cbdv.202100464   
2021 Golysheva EA, Boyle AL, Biondi B, Ruzza P, Kros A, Raap J, Toniolo C, Formaggio F, Dzuba SA. Probing the E/K Peptide Coiled-Coil Assembly by Double Electron-Electron Resonance and Circular Dichroism. Biochemistry. 60: 19-30. PMID 33320519 DOI: 10.1021/acs.biochem.0c00773   
2021 Banerjee R, Sheet T, Banerjee S, Biondi B, Formaggio F, Toniolo C, Peggion C. C-Methyl-l-valine: A Preferential Choice over α-Aminoisobutyric Acid for Designing Right-Handed α-Helical Scaffolds. Biochemistry. PMID 34463474 DOI: 10.1021/acs.biochem.1c00340   
2021 Sepehri A, Nepal B, Lazaridis T. Distinct Modes of Action of IAPP Oligomers on Membranes. Journal of Chemical Information and Modeling. PMID 34499498 DOI: 10.1021/acs.jcim.1c00767   
2021 Yin R, Guest JD, Taherzadeh G, Gowthaman R, Mittra I, Quackenbush J, Pierce BG. Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants. Plos Computational Biology. 17: e1009380. PMID 34491988 DOI: 10.1371/journal.pcbi.1009380   
2021 Pandey B, Dev A, Chakravorty D, Bhandare VV, Polley S, Roy S, Basu G. Insights on the disruption of the complex between human positive coactivator 4 and p53 by small molecules. Biochemical and Biophysical Research Communications. 578: 15-20. PMID 34534740 DOI: 10.1016/j.bbrc.2021.09.020   
2021 Vardar G, Salazar-Lázaro A, Brockmann MM, Weber-Boyvat M, Zobel S, Kumbol VW, Trimbuch T, Rosenmund C. Reexamination of N-terminal domains of Syntaxin-1 in vesicle fusion from central murine synapses. Elife. 10. PMID 34427183 DOI: 10.7554/eLife.69498   
2021 Cao Y, Choi YK, Frank M, Woo H, Park SJ, Yeom MS, Seok C, Im W. Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies. Journal of Chemical Theory and Computation. PMID 34529436 DOI: 10.1021/acs.jctc.1c00552   
2021 Bageshwar UK, DattaGupta A, Musser SM. Influence of the TorD signal peptide chaperone on Tat-dependent protein translocation. Plos One. 16: e0256715. PMID 34499687 DOI: 10.1371/journal.pone.0256715   
2021 Pace JR, Lampkin BJ, Abakah C, Moyer A, Miao J, Deprey K, Cerulli RA, Lin YS, Baleja JD, Baker D, Kritzer JA. Stapled β-Hairpins Featuring 4-Mercaptoproline. Journal of the American Chemical Society. PMID 34516087 DOI: 10.1021/jacs.1c04378   
2021 Jung J, Bong JH, Sung JS, Lee SJ, Lee M, Kang MJ, Jose J, Pyun JC. Fluorescein and Rhodamine B-Binding Domains from Autodisplayed Fv-Antibody Library. Bioconjugate Chemistry. PMID 34617729 DOI: 10.1021/acs.bioconjchem.1c00376   
2021 Hassankalhori M, Bolcato G, Bissaro M, Sturlese M, Moro S. Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics. Frontiers in Molecular Biosciences. 8: 707661. PMID 34532343 DOI: 10.3389/fmolb.2021.707661   
2021 Feng R, Ni R, Chau Y. Altered Peptide Self-Assembly and Co-Assembly with DNA by Modification of Aromatic Residues. Chemmedchem. PMID 34528415 DOI: 10.1002/cmdc.202100440   
2021 He L, Gao Y, Wang X, Han L, Yu Q, Shi H, Song R. Ultrasonication promotes extraction of antioxidant peptides from oxhide gelatin by modifying collagen molecule structure. Ultrasonics Sonochemistry. 78: 105738. PMID 34509958 DOI: 10.1016/j.ultsonch.2021.105738   
2021 Xu Y, Knapp K, Le KN, Schafer NP, Safari MS, Davtyan A, Wolynes PG, Vekilov PG. Frustrated peptide chains at the fibril tip control the kinetics of growth of amyloid-β fibrils. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34518234 DOI: 10.1073/pnas.2110995118   
2021 Lei J, Cai M, Shen Y, Lin D, Deng X. Molecular dynamics study on the inhibition mechanisms of ReACp53 peptide for p53-R175H mutant aggregation. Physical Chemistry Chemical Physics : Pccp. PMID 34612239 DOI: 10.1039/d1cp03094a   
2021 Kar M, Posey AE, Dar F, Hyman AA, Pappu RV. Glycine-Rich Peptides from FUS Have an Intrinsic Ability to Self-Assemble into Fibers and Networked Fibrils. Biochemistry. PMID 34648275 DOI: 10.1021/acs.biochem.1c00501   
2021 Maben Z, Arya R, Georgiadis D, Stratikos E, Stern LJ. Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism. Nature Communications. 12: 5302. PMID 34489420 DOI: 10.1038/s41467-021-25564-w   
2021 Zhang W, Liu J, Zhang C, Yu X, Zhong B. Structural definition of the discrete hotspot sites of BMP-2 conformational wrist epitope and rational design of the hotspot-derived osteogenic peptides against chondrocyte senescence. Bioorganic Chemistry. 116: 105382. PMID 34598087 DOI: 10.1016/j.bioorg.2021.105382   
2021 Qu S, Wang X, Yang L, Meng R, Feng C, Yang B, Huang J, Li Q, Wang J, Zhang D. Mapping of a unique epitope on domain III of the envelope protein of Tembusu virus. Virus Research. 198582. PMID 34599934 DOI: 10.1016/j.virusres.2021.198582   
2021 Zegota MM, Müller MA, Lantzberg B, Kizilsavas G, Coelho JAS, Moscariello P, Martínez-Negro M, Morsbach S, Gois PMP, Wagner M, Ng DYW, Kuan SL, Weil T. Dual Stimuli-Responsive Dynamic Covalent Peptide Tags: Toward Sequence-Controlled Release in Tumor-like Microenvironments. Journal of the American Chemical Society. PMID 34632780 DOI: 10.1021/jacs.1c06559   
2021 Akiba H, Tamura H, Caaveiro JMM, Tsumoto K. Epitope-dependent thermodynamic signature of single-domain antibodies against hen egg lysozyme. Journal of Biochemistry. PMID 34519785 DOI: 10.1093/jb/mvab082   
2021 Phillips AM, Lawrence KR, Moulana A, Dupic T, Chang J, Johnson MS, Cvijovic I, Mora T, Walczak AM, Desai MM. Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies. Elife. 10. PMID 34491198 DOI: 10.7554/eLife.71393   
2021 Cerutti G, Guo Y, Wang P, Nair MS, Wang M, Huang Y, Yu J, Liu L, Katsamba PS, Bahna F, Reddem ER, Kwong PD, Ho DD, Sheng Z, Shapiro L. Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain. Cell Reports. 109928. PMID 34706271 DOI: 10.1016/j.celrep.2021.109928   
2021 Banach BB, Cerutti G, Fahad AS, Shen CH, Oliveira De Souza M, Katsamba PS, Tsybovsky Y, Wang P, Nair MS, Huang Y, Francino-Urdániz IM, Steiner PJ, Gutiérrez-González M, Liu L, López Acevedo SN, et al. Paired heavy- and light-chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses. Cell Reports. 109771. PMID 34587480 DOI: 10.1016/j.celrep.2021.109771   
2021 Li T, Xue W, Zheng Q, Song S, Yang C, Xiong H, Zhang S, Hong M, Zhang Y, Yu H, Zhang Y, Sun H, Huang Y, Deng T, Chi X, et al. Cross-neutralizing antibodies bind a SARS-CoV-2 cryptic site and resist circulating variants. Nature Communications. 12: 5652. PMID 34580306 DOI: 10.1038/s41467-021-25997-3   
2021 Dong J, Zost SJ, Greaney AJ, Starr TN, Dingens AS, Chen EC, Chen RE, Case JB, Sutton RE, Gilchuk P, Rodriguez J, Armstrong E, Gainza C, Nargi RS, Binshtein E, et al. Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail. Nature Microbiology. PMID 34548634 DOI: 10.1038/s41564-021-00972-2   
2021 Mule SN, Rosa-Fernandes L, Coutinho JVP, Gomes VM, Macedo-da-Silva J, Santiago VF, Quina D, de Oliveira GS, Thaysen-Andersen M, Larsen MR, Labriola L, Palmisano G. Systems-wide analysis of glycoprotein conformational changes by limited deglycosylation assay. Journal of Proteomics. 248: 104355. PMID 34450331 DOI: 10.1016/j.jprot.2021.104355   
2021 Zhang P, Gao J, Che H, Xue W, Yang D. Molecular Basis of IgE-Mediated Shrimp Allergy and Heat Desensitization. Nutrients. 13. PMID 34684397 DOI: 10.3390/nu13103397