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Polarity of the P1 anchor residue determines peptide binding specificity between HLA-A*3101 and HLA-A*3303.

• Authors : Takiguchi, M.; Matsuda, T.; Tomiyama, H.

• Source: Tissue Antigens. Dec2000, Vol. 56 Issue 6, p501. 6p. 4 Charts, 4 Graphs.

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TCR-induced alteration of primary MHC peptide anchor residue

• Authors : Madura, Florian; Rizkallah, Pierre J.; Legut, Mateusz

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Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps

• Authors : Perumal, Senthil K.; Xu, Xiaojun; Yan, Chunli ...

• Source: Journal of Molecular Biology ; volume 431, issue 14, page 2493-2510 ; ISSN 0022-2836

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Binding of peptides lacking consensus anchor residue alters H-2Ld serologic recognition

• Authors : Solheim, Joyce C.; Carreño, Beatriz M.; Smith, Joseph D.

Subjects: Article

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Ricin uses arginine 235 as an anchor residue to bind to P-proteins of the ribosomal stalk

• Authors : Zhou, Yijun; Li, Xiao-Ping; Chen, Brian Y.

• Source: Scientific Reports ; volume 7, issue 1 ; ISSN 2045-2322

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Structural basis for ineffective T‐cell responses to MHC anchor residue‐improved “heteroclitic” peptides

• Authors : Madura, Florian; Rizkallah, Pierre J.; Holland, Christopher J. ...

• Source: European Journal of Immunology ; volume 45, issue 2, page 584-591 ; ISSN 0014-2980 1521-4141

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Increased Diversity of the HLA-B40 Ligandome by the Presentation of Peptides Phosphorylated at Their Main Anchor Residue.

• Authors : Marcilla, Miguel; Alpízar, Adán; Lombardía, Manuel

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Identification of an Anchor Residue for CheA-CheY Interactions in the Chemotaxis System of Escherichia coli

• Authors : Thakor, Hemang; Nicholas, Sarah; Porter, Ian M.

• Source: Journal of Bacteriology ; volume 193, issue 15, page 3894-3903 ; ISSN 0021-9193 1098-5530

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Polarity of the P1 anchor residue determines peptide binding specificity between HLA-A*3101 and HLA-A*3303

• Authors : Hiroko Tomiyama; Tomoko Matsuda; Masafumi Takiguchi

Subjects: chemistry.chemical_classification; Polarity (international relations); Sequence analysis

• Source: Tissue Antigens. 56:501-506

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Cells in Patients Following Vaccination with a Peptide Modified at an HLA-A2.1 Anchor Residue

• Authors : Timothy M. Clay; Mary C. Custer; Mark D. Mckee ...

• Source: http://www.jimmunol.org/content/162/3/1749.full.pdf.

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Importance of Aromatic Anchor Residue Identity and Location for the Tilt and Dynamics of Transmembrane Peptides

• Authors : Gist, Renetra R.; Gleason, Nicholas J.; Langston, Rebekah

• Source: Biophysical Journal ; volume 102, issue 3, page 76a ; ISSN 0006-3495

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Structural studies of PI3K SH3 domain in complex with a peptide ligand: role of anchor residue in ligand binding

• Authors : Batra-Safferling, R.; Granzin, J.; Moedder, S.

Subjects: info:eu-repo/classification/ddc/540; Amino Acid Sequence; Binding SitesDE

• Source: Biological chemistry 391, 33 - 42 (2010). doi:10.1515/bc.2010.003

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Charged or Aromatic Anchor Residue Dependence of Transmembrane Peptide Tilt

• Authors : Vostrikov, Vitaly V.; Daily, Anna E.; Greathouse, Denise V.

• Source: Journal of Biological Chemistry ; volume 285, issue 41, page 31723-31730 ; ISSN 0021-9258

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Cutting edge: a single MHC anchor residue alters the conformation of a peptide-MHC complex inducing T cells that survive negative selection

• Authors : Daniel A. Peterson; Richard J. Dipaolo; Osami Kanagawa ...

• Source: http://jimmunol.highwire.org/content/166/10/5874.full.pdf.

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Brain-Infiltrating Cytolytic T Lymphocytes Specific for Theiler’s Virus Recognize H2D b Molecules Complexed with a Viral VP2 Peptide Lacking a Consensus Anchor Residue

• Authors : Nancy D. Borson; Claire Paul; Xiaoqi Lin ...

• Source: http://jvi.asm.org/content/71/7/5244.full.pdf.

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Brain-infiltrating cytolytic T lymphocytes specific for Theiler's virus recognize H2Db molecules complexed with a viral VP2 peptide lacking a consensus anchor residue

• Authors : Borson, N D; Paul, C; Lin, X

• Source: Journal of Virology ; volume 71, issue 7, page 5244-5250 ; ISSN 0022-538X 1098-5514

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Toward Guided Mutagenesis: Gaussian Process Regression Predicts MHC Class II Antigen Mutant Binding

• Authors : David R. Bell (1978681); Serena H. Chen (7047176)

Subjects: Biophysics; Biochemistry; Microbiology

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Quantitation of peptide anchor residue contributions to class I major histocompatibility complex molecule binding.

• Authors : Saito, Y; Peterson, P.A.; Matsumura, M

• Source: Journal of Biological Chemistry ; volume 268, issue 28, page 21309-21317 ; ISSN 0021-9258

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Figure 1. General mechanism for ligand binding to flexible receptor. ; In the conformational selection pathway, the ligand docks to the bound-like (BL) form of the apo receptor (apoBL) to form the bound-like encounter complex (ECBL). In the induced fit pathway, the ligand docks to the non-bound-like (NBL) form of the apo receptor (apoNBL) to form the non-bound-like encounter complex (ECNBL). Intermolecular interactions then drive structural transitions to the ECBL. Both pathways end with a final induced fit step that optimizes interface side chains, transitioning to the high-affinity complex (HAC). The binding mechanism also highlights an anchor residue often found to be important in molecular recognition (Rajamani et al., 2004).

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Figure 2. Flexibility of the PD-1 binding interface. ; (a) The apo PD-1 binding interface (Cheng et al., 2013), showing a flat, polar, core binding interface. Surface residues that shape the core binding interface are labelled. (b) The core PD-1 (green) - PD-L1 (yellow) binding interface, showing a flat hydrophobic receptor surface (Zak et al., 2015). White dashed lines indicate hydrogen bonds between PD-L1 side chains. (c) The core PD-1 (cyan) – PD-L2 (orange) binding interface, showing a large hydrophobic receptor cavity (Lázár-Molnár et al., 2008). White dashed lines indicate hydrogen bonds between PD-L2 side chains. Note that the conserved anchor residue Tyr123/112 is present in both (b) and (c). (d) Fractional occlusion of each bound-like Trp110 and Tyr123/112 atom position in the NMR ensemble of apo PD-1. Numerical values at each atom position denote the fraction of NMR frames that overlap, or ‘occlude’, that position (see Materials and methods for full details of how fractional occlusion is calculated). Aside from the Cβ, the Trp110 pocket is mostly occluded in the apo PD-1 ensemble, whereas the Tyr123/112 anchor pocket is largely open. (e) Overlay of apo, PD-L1–bound, and PD-L2–bound structures of PD-1 defining the ‘open’ and ‘closed’ states of PD-1 residues Asn66 and Ile126 in relation to the open and closed states of the Trp110 binding pocket.

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Modifications in Immune Response Patterns Induced by Kynurenine and One-Residue-Substituted T Cell Epitopes in SARS-CoV-2-Specific Human T Cells.

• Authors : Tokano, Mieko^1,2,3 (AUTHOR) ; Takagi, Rie¹ (AUTHOR); Matsushita, Sho^1,3 (AUTHOR)

• Source: COVID. Oct2024, Vol. 4 Issue 10, p1676-1683. 8p.

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Probing protein flexibility reveals a mechanism for selective promiscuity

• Authors : Nicolas A Pabon; Carlos J Camacho

Subjects: PD-1; induced fit; specificity

• Source: eLife, Vol 6 (2017)

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3′dNTP Binding Is Modulated during Primer Synthesis and Translesion by Human PrimPol.

• Authors : Velázquez-Ruiz, Cristina¹ (AUTHOR) ; Blanco, Luis¹ (AUTHOR) ; Martínez-Jiménez, María Isabel¹ (AUTHOR)

Subjects: *DNA synthesis; *DNA primers; *DNA replication

• Source: International Journal of Molecular Sciences. Jan2024, Vol. 25 Issue 1, p51. 20p.

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Anchoring Intrinsically Disordered Proteins to Multiple Targets: Lessons from N-Terminus of the p53 Protein

• Authors : Yongqi Huang; Zhirong Liu

Subjects: anchor residue; intrinsically disordered proteins; binding promiscuityagris

• Source: International Journal of Molecular Sciences; Volume 12; Issue 2; Pages: 1410-1430

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www.mdpi.com/journal/ijms Anchoring Intrinsically Disordered Proteins to Multiple Targets: Lessons from N-Terminus of the p53 Protein

• Authors : Yongqi Huang; Zhirong Liu; The Pennsylvania State University CiteSeerX Archives

Subjects: anchor residue; intrinsically disordered proteins; binding promiscuity

• Source: ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/ec/48/Int_J_Mol_Sci_2011_Feb_23_12(2)_1410-1430.tar.gz

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Evidence of hiv-1 adaptation to host hla alleles following chimp-to-human transmission

• Authors : Ngandu, Nobubelo K; Seoighe, Cathal; Scheffler, Konrad

Subjects: immunodeficiency-virus type-1; anchor residue motifs; disease progression

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Crystal Structure of a Classical MHC Class I Molecule in Dogs; Comparison of DLA-88*0 and DLA-88*5 Category Molecules.

• Authors : Sun, Yujiao¹ (AUTHOR); Ma, Lizhen^2,3 (AUTHOR); Li, Shen² (AUTHOR)

• Source: Cells (2073-4409). Apr2023, Vol. 12 Issue 7, p1097. 16p.

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QM/MM Study of Epitope Peptides Binding to HLA-A*0201: The Roles of Anchor Residues and Water.

• Authors : Yuanchao Li¹ ; Yadong Yang²; Ping He³

• Source: Chemical Biology & Drug Design. Dec2009, Vol. 74 Issue 6, p611-618. 8p. 4 Diagrams, 3 Charts, 1 Graph.

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Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota.

• Authors : Blank, P. N.¹ (AUTHOR); Barnett, A. A.² (AUTHOR); Ronnebaum, T. A.¹ (AUTHOR)

• Source: Acta Crystallographica: Section D, Structural Biology. Jun2020, Vol. 76 Issue 6, p542-557. 16p.

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Ca2+/calmodulin-dependent regulation of polycystic kidney disease 2-like-1 by binding at C-terminal domain.

• Authors : Julia Young Baik¹; Eunice Yon June Park¹; Insuk So¹

• Source: Korean Journal of Physiology & Pharmacology. May2020, Vol. 24 Issue 3, p277-286. 10p.

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Anchoring Intrinsically Disordered Proteins to Multiple Targets: Lessons from N-Terminus of the p53 Protein

• Authors : Zhirong Liu; Yongqi Huang

Subjects: p53; anchor residue; intrinsically disordered proteins

• Source: International Journal of Molecular Sciences, Vol 12, Iss 2, Pp 1410-1430 (2011)International Journal of Molecular Sciences; Volume 12; Issue 2; Pages: 1410-1430International Journal of

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Molecular Stapling of Human Pediatric RSV Phosphoprotein’s C-terminal Tail-Derived Peptides to Target the Coupled Folding-Upon-Binding Event Between Phosphoprotein and Nucleocapsid.

• Authors : Zhang, Leling¹ (AUTHOR); Gong, Yong¹ (AUTHOR); Shen, Lili¹ (AUTHOR)

• Source: International Journal of Peptide Research & Therapeutics. Feb2023, Vol. 29 Issue 1, p1-8. 8p.

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Computational Structural and Functional Analyses of ORF10 in Novel Coronavirus SARS-CoV-2 Variants to Understand Evolutionary Dynamics.

• Authors : Mishra, Seema¹ (AUTHOR)

• Source: Evolutionary Bioinformatics. 7/7/20222, Vol. 18, p1-14. 14p.

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Interleukin‐25 recognition by its unique receptor IL‐17Rb via two discrete linear and cyclic epitopes.

• Authors : Wu, Tao¹ (AUTHOR); Ma, Huaijun² (AUTHOR); He, Ping² (AUTHOR)

• Source: Chemical Biology & Drug Design. Mar2022, Vol. 99 Issue 3, p382-390. 9p.

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Machine learning optimization of peptides for presentation by class II MHCs

• Authors : Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory; Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science; Massachusetts Institute of Technology. Department of Biological Engineering

Subjects: Article; http://purl.org/eprint/type/JournalArticle

• Source: Oxford University Press

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Identities of P2 and P3 Residues of H-2Kb-Bound Peptides Determine Mouse Ly49C Recognition.

• Authors : Marquez, Elsa A.¹; Kane, Kevin P.¹

Subjects: *PEPTIDES; *LABORATORY mice; *MAJOR histocompatibility complex

• Source: PLoS ONE. 7/6/2015, Vol. 10 Issue 7, p1-17. 17p.

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3′dNTP Binding Is Modulated during Primer Synthesis and Translesion by Human PrimPol

• Authors : Velázquez-Ruiz, Cristina; Blanco, Luis; Martínez-Jiménez, María Isabel

Subjects: artículo

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Modifications in Immune Response Patterns Induced by Kynurenine and One-Residue-Substituted T Cell Epitopes in SARS-CoV-2-Specific Human T Cells

• Authors : Mieko Tokano; Rie Takagi; Sho Matsushita

Subjects: CD4+ T cells; COVID-19; IL-8

• Source: COVID, Vol 4, Iss 10, Pp 1676-1683 (2024)

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Crystal structure of Qa-1a with bound Qa-1 determinant modifier peptide.

• Authors : Ying, Ge¹; Wang, Jing¹; Kumar, Vipin²

Subjects: *MAJOR histocompatibility complex; *T cells; *KILLER cells

• Source: PLoS ONE. 8/2/2017, Vol. 12 Issue 8, p1-12. 12p.

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Structural and Functional Analysis of PGRP-LC Indicates Exclusive Dap-Type PGN Binding in Bumblebees.

• Authors : Liu, Yanjie¹ (AUTHOR) ; Ye, Nanhui² (AUTHOR) ; Chen, Minming² (AUTHOR)

Subjects: *BUMBLEBEES; *HONEYBEES; *FUNCTIONAL analysis

• Source: International Journal of Molecular Sciences. Apr2020, Vol. 21 Issue 7, p2441. 1p. 2 Diagrams, 1 Chart, 2 Graphs.

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The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study.

• Authors : Abualrous, Esam Tolba^1,2; Saini, Sunil Kumar¹; Ramnarayan, Venkat Raman¹

Subjects: *MAJOR histocompatibility complex; *PEPTIDE analysis; *MOLECULAR dynamics

• Source: PLoS ONE. 8/13/2015, Vol. 10 Issue 8, p1-17. 17p.

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Machine learning optimization of peptides for presentation by class II MHCs

• Authors : Dai, Zheng; Huisman, Brooke D; Zeng, Haoyang ...

• Source: Oxford University Press

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Disruption of Hydrogen Bonds between Major Histocompatibility Complex Class II and the Peptide N-Terminus Is Not Sufficient to Form a Human Leukocyte Antigen-DM Receptive State of Major Histocompatibility Complex Class II

• Authors : Sadegh-Nasseri, S; Schulze, M-SED; Anders, A-K

Subjects: Journal Article

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Structural basis for self-discrimination by neoantigen-specific TCRs

• Authors : John P. Finnigan; Jenna H. Newman; Yury Patskovsky

Subjects: Science

• Source: Nature Communications, Vol 15, Iss 1, Pp 1-18 (2024)

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Structural and Functional Analysis of PGRP-LC Indicates Exclusive Dap-Type PGN Binding in Bumblebees

• Authors : Yanjie Liu; Nanhui Ye; Minming Chen

Subjects: PGRP-LC; bumblebee; Bombus lantschouensisagris

• Source: International Journal of Molecular Sciences; Volume 21; Issue 7; Pages: 2441

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Dimorphic HLA- B signal peptides differentially influence HLA- E- and natural killer cell-mediated cytolysis of HIV-1-infected target cells.

• Authors : Merino, A. M.^1,2; Sabbaj, S.¹; Easlick, J.²

Subjects: *HLA histocompatibility antigens; *SIGNAL peptides; *KILLER cells

• Source: Clinical & Experimental Immunology. Dec2013, Vol. 174 Issue 3, p414-423. 10p.

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Munc13-Like skMLCK Variants Cannot Mimic the Unique Calmodulin Binding Mode of Munc13 as Evidenced by Chemical Cross-Linking and Mass Spectrometry.

• Authors : Herbst, Sabine¹; Maucher, Daniel¹; Schneider, Marian²

Subjects: *CALMODULIN; *MASS spectrometry; *PRESYNAPTIC receptors

• Source: PLoS ONE. Oct2013, Vol. 8 Issue 10, p1-11. 11p.

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Identification of a novel variant of LMP-1 of EBV in patients with endemic Burkitt lymphoma in western Kenya.

• Authors : Wohlford, Eric M.¹ (AUTHOR); Asito, Amolo S.^2,3 (AUTHOR); Chelimo, Kiprotich^2,4 (AUTHOR)

• Source: Infectious Agents & Cancer. 2013, Vol. 8 Issue 1, p34-42. 9p. 2 Diagrams, 2 Charts, 3 Graphs.

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Prevention of Cytotoxic T Cell Escape Using a Heteroclitic Subdominant Viral T Cell Determinant.

• Authors : Butler, Noah S.^1,2; Alex Theodossis³; Andrew I. Webb⁴

• Source: PLoS Pathogens. Oct2008, Vol. 4 Issue 10, p1-13. 13p. 2 Diagrams, 2 Charts, 4 Graphs.

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Stable Cytotoxic T Cell Escape Mutation in Hepatitis C Virus Is Linked to Maintenance of Viral Fitness.

• Authors : Uebelhoer, Luke¹; Jin-Hwan Han²; Callendret, Benoit^3,4

• Source: PLoS Pathogens. Sep2008, Vol. 4 Issue 9, p1-15. 15p. 7 Graphs.

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