Structural and functional characterisation of the collagen binding domain of fibronectin by Millard, CJ

“…However, the presence of at least a single GlcNAc sugar residue on the second sugar chain site on 8Fn1 (N- linked to N511) is essential for full affinity binding to collagen. Direct binding of the 8Fn1-9Fn1 module pair to collagen is assessed with a short collagen peptide and the binding is monitored by NMR. …”

Mapping the structural and dynamical features of multiple p53 DNA binding domains : insights into loop 1 intrinsic dynamics by Lukman, Suryani., Lane, David P., Verma, Chandra S.

“…Loop 1 occupies two major conformational states: extended and recessed; the former but not the latter displays correlations in atomic fluctuations with those of loop 2 (~24 Å apart). Since loop 1 binds to the major groove whereas loop 2 binds to the minor groove of DNA, our results begin to provide some insight into the possible mechanism underpinning the cooperative nature of DBD binding to DNA. …”
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21W.730-2 Expository Writing - Food for Thought: Writing and Reading about Food and Culture, Fall 2005 by Boiko, Karen

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Induction of z-conformation in ribosomal RNA by Z-DNA binding domain Zα of the human double-stranded RNA deaminase I (ADAR1) by Zhao, Jing

“…Therefore, our theoretical model shall predict whether the chemical shifts perturbations observed through the small binding partner can be used to delineate the involved binding interface, and whether changes of the positions of NMR resonances or only attenuation of the cross-peak intensities are to be expected upon binding to a solid partner.…”
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Nutraceuticals silybin B, resveratrol, and epigallocatechin-3 gallate-bind to cardiac muscle troponin to restore the loss of lusitropy caused by cardiomyopathy mutations in vitro,... by Yang, Z, Sheehan, AM, Messer, AE, Tsui, S, Sparrow, A, Redwood, C, Kren, V, Gould, IR, Marston, SB

“…Results: Silybin B, EGCG and resveratrol restored the phosphorylation-induced change in molecular dynamics to wild-type values, whilst silybin A, an inactive isomer of silybin B, and Epicatechin gallate, an EGCG analogue that does not recouple, did not. …”

Myopathy-causing Q147P TPM2 mutation shifts tropomyosin strands further towards the open position and increases the proportion of strong-binding cross-bridges during the ATPase cyc... by Karpicheva, OE, Simonyan, AO, Kuleva, NV, Redwood, CS, Borovikov, YS

“…Despite its reduced affinity for actin in co-sedimentation assay, the Q147P mutant incorporates into the muscle fiber. However, compared to wild-type tropomyosin, it locates closer to the center of the actin filament. …”

The role of growth factor receptor bound protein 2 (GRB2) in gain of function of mutant p53. by Lau, Sok Ting.

“…In this study, GRB2, a binding partner of mutant p53 was explored to uncover its role in mutant p53 “gain-of-function”. …”
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Computational investigations of HIV-1 protease and protease inhibitors interactions by Sham, Hoi Fung

“…Both wild type HIV-1 proteases and mutated HIV-1 proteases were used in the docking simulations. …”
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Recognition of A-U and U-A base pairs in RNA duplexes by modified peptide nucleic acids by Yuan, Zhen

“…Fluorescence binding studies were carried out to measure the binding affinity at physiological pH conditions. …”
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Structural basis of haptoglobin-haemoglobin scavenging by CD163 by Zhou, X

“…Indeed, biophysical assays show that calcium ions are critical for ligand binding. Mutational studies demonstrate that while monomeric CD163 can scavenge the multimeric Hp(2-2)Hb, uptake of the dimeric Hp(1-1)Hb and Hb is impaired compared to the wild-type receptor, suggesting that receptor multimerisation evolved to facilitate uptake of lower affinity ligands. …”

Thermal induced coupling of cell adhesion/deadhesion and migration under HBV replication and EGCG treatment by Li, Xi

“…In the first part of my thesis, TRP was applied as a model system for elucidating the effect of HBV replication on the biophysical responses of HepG2 cells transfected by wild type HBV genome. Moreover, mutant HBV genome is designed to assess the specific activity of the SH3-binding domain of HBx during HBV replication. …”
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Site-specific protein modifications by an engineered asparaginyl endopeptidase from Viola canadensis by Chen, Yu, Zhang, Dingpeng, Zhang, Xiaohong, Wang, Zhen, Liu, Chuan-Fa, Tam, James P.

“…Wild type VcAEP yields <5% cyclic product from a linear substrate at pH 6.5, whereas the single mutants VcAEP-V238A (Vc1a) and VcAEP-Y168A (Vc1b) targeting the S2 and S1' substrate-binding pockets yielded 34 and 61% cyclic products, respectively. …”
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Structural features that affect β2 integrin expression and regulation of adhesion by Guan, Siyu

“…(It should be noted that wild-type LFA-1 requires one activating agent to bind ICAM-1 and two to bind ICAM-3.) …”
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Effects of clozapine-N-oxide and compound 21 on sleep in laboratory mice by Traut, J, Mengual, JP, Meijer, E, McKillop, L, Alfonsa, H, Hoerder-Suabedissen, A, Song, SH, Fehér, KD, Riemann, D, Molnar, Z, Akerman, CJ, Vyazovskiy, VV, Krone, LB

“…Effects of CNO on sleep could arise from back-metabolism to clozapine or binding to endogenous neurotransmitter receptors. …”

Biomolecular hydration in protein-protein interaction, protein stability and aggregation and lead optimization : computational studies by Mohan Rajan Pradhan

“…Driven by the observation that restoring the wild type function of mutant p53 is known to prevent tumors, I am in the process of screening libraries of compounds against this new pocket to identify binders that may guide the development of molecules to restabilize mutant p53. …”
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Identification of novel functional compounds from forest onion and its biological activities against breast cancer by Nurkolis, Fahrul, Kurniatanty, Isma, Wiyarta, Elvan, Permatasari, Happy Kurnia, Mayulu, Nelly, Taslim, Nurpudji Astuti, Tjandrawinata, Raymond Rubianto, Hardinsyah, Hardinsyah, Tallei, Trina Ekawati, Tsopmo, Apollinaire, Radu, Son, Hadinata, Edwin, Kim, Bonglee, Ribeiro, Rosy Iara Maciel Azambuja, Syahputra, Rony Abdi

“…A natural resource with potential activity against breast cancer is forest onion, Eleutherine bulbosa (Mill.) Urb., but the identity of its active constituents and their mechanisms of action remain unexplored. …”
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Phosphatidylinositol 4,5-Bisphosphate Is an HCV NS5A Ligand and Mediates Replication of the Viral Genome by Cho, Nam-Joon, Lee, Choongho, Pang, Phillip S., Pham, Edward A., Fram, Benjamin, Nguyen, Khanh, Xiong, Anming, Sklan, Ella H., Elazar, Menashe, Koytak, Elif S., Kersten, Caroline, Kanazawa, Kay K., Frank, Curtis W., Glenn, Jeffrey S.

“…Methods: We used a combination of quartz crystal microbalance, circular dichroism, molecular genetics, and immunofluorescence to study specific binding of PI(4,5)P2 by the HCV NS5A protein. We evaluated the effects of PI(4,5)P2 on the function of NS5A by expressing wild-type or mutant forms of Bart79I or FL-J6/JFH-5’C19Rluc2AUbi21 RNA in Huh7 cells. …”
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The molecular pathogenesis of FUS mutations in amyotrophic lateral sclerosis using in vivo and in vitro models by Kent, L

“…Fused in sarcoma (FUS) is an RNA binding protein, and mutations in the FUS gene are responsible for approximately 4% of familial and &amp;LT;1% of sporadic ALS cases. …”

Selectivity of stop codon recognition in translation termination is modulated by multiple conformations of GTS loop in eRF1 by Li, Yan, Pillay, Shubhadra, Frolova, Ludmila, Pervushin, Konstantin, Wong, Leo E.

“…By solving the solution structures of the wild-type N-domain of human eRF1 exhibited omnipotent specificity, i.e. recognition of all three stop codons, and its unipotent mutant with UGA-only specificity, we found the conserved GTS loop adopting alternate conformations. …”
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Investigating the role of CDK1 in governing the transcriptional landscape in cancer cells by Pluta, AJ

“…Subsequent analysis of the upregulated genes identified several transcription factors as candidates for involvement in mediating the transcriptional effects of CDK1 across different cell types, after their binding motifs were found to be enriched upstream of the transcription start site of the dysregulated genes. …”