Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation

Journal of Virology

Volumn 76, Issue 17, 2002, Pages 8757-8768

  Yusim, Karina ^a   Kesmir, Can ^a   Gaschen, Brian ^a   Addo, Marylyn M ^a   Altfeld, Marcus ^a   Brunak, Søren ^a   Chigaev, Alexandre ^a   Detours, Vincent ^a   Korber, Bette T ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HLA ANTIGEN; VIRUS PROTEIN;

ALPHA HELIX; ARTICLE; CARBOXY TERMINAL SEQUENCE; CLONAL ANERGY; CLUSTER ANALYSIS; COMPLEX FORMATION; CYTOTOXIC T LYMPHOCYTE; ENDOPLASMIC RETICULUM; GENOME IMPRINTING; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; VIRUS CELL INTERACTION; VIRUS REPLICATION;

AMINO ACID SEQUENCE; ANTIGENIC VARIATION; CYSTEINE ENDOPEPTIDASES; EPITOPE MAPPING; EPITOPES, T-LYMPHOCYTE; HIV INFECTIONS; HIV-1; HUMANS; MULTIENZYME COMPLEXES; PROTEASOME ENDOPEPTIDASE COMPLEX; SEQUENCE ALIGNMENT; T-LYMPHOCYTES, CYTOTOXIC; VARIATION (GENETICS); VIRAL PROTEINS;

EID: 0036340475     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.76.17.8757-8768.2002     Document Type: Article

References (67)

1. Function of the transport complex TAP in cellular immune recognition
2. The HIV-1 regulatory proteins Tat and Rev are frequently targeted by cytotoxic T lymphocytes derived from HIV-1-infected individuals
3. Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia
4. Vpr is preferentially targeted by CTL during HIV-1 infection
5. The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling
6. Solution structure of a polypeptide from the N terminus of the HIV protein Nef
7. DNA vaccination for HIV-1 and SIV
8. The Pfam protein families database
9. Abrogation of CTL epitope processing by single amino acid substitution flanking the C-terminal proteasome cleavage site
10. Molecular mapping of a histocompatibility-restricted immunodominant T cell epitope with synthetic and natural peptides: Implications for T cell antigenic structure
11. Human immunodeficiency virus (HIV)-specific cytotoxic T lymphocyte activity in HIV-exposed seronegative persons
12. Head-to-tail dimers and interdomain flexibility revealed by the crystal structure of HIV-1 capsid protein (p24) complexed with a monoclonal antibody Fab
13. Protein antigenic structures recognized by T cells: Potential applications to vaccine design
14. Human immunodeficiency virus type 1-specific cytotoxic T lymphocyte activity is inversely correlated with HIV type 1 viral load in HIV type 1-infected long-term survivors
15. The proteasome
16. Resistance to antiretroviral drugs in patients with primary HIV-1 infection
17. The flexibility of the TCR allows recognition of a large set of naturally occurring epitope variants by HIV-specific cytotoxic T lymphocytes
18. PeptGen: Designing peptides for immunological studies and application to HIV consensus sequences
19. Cytotoxic T-lymphocyte cross-reactivity among different human immunodeficiency virus type 1 clades: Implications for vaccine development
20. Altered properties of the branched chain amino acid-preferring activity contribute to increased cleavages after branched chain residues by the "immunoproteasome."
21. Dendritic cells transfected with the nef genes of HIV-1 primary isolates specifically activate cytotoxic T lymphocytes from seropositive subjects
22. Relationship between peptide selectivities of human transporters associated with antigen processing and HLA class I molecules
23. Relative dominance of epitope-specific cytotoxic T-lymphocyte responses in human immunodeficiency virus type 1-infected persons with shared HLA alleles
24. From genome to vaccine: In silico predictions, ex vivo verification
25. Simian immunodeficiency virus (SIV) gag DNA-vaccinated rhesus monkeys develop secondary cytotoxic T-lymphocyte responses and control viral replication after pathogenic SIV infection
26. The human 26S and 20S proteasomes generate overlapping but different sets of peptide fragments from a model protein substrate
27. Hierarchies of antigen-specific cytotoxic T-cell responses
28. A giant protease with potential to substitute for some functions of the proteasome
29. Protection against human immunodeficiency virus type 1 infection in persons with repeated exposure: Evidence for T cell immunity in the absence of inherited CCR5 coreceptor defects
30. Co-evolution of human immunodeficiency virus and cytotoxic T-lymphocyte responses
31. Rapid characterization of HIV clade C-specific cytotoxic T lymphocyte responses in infected African children and adults
32. Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS
33. Antigen presentation in extracellular matrix: Interactions of T cells with dendritic cells are dynamic, short lived, and sequential
34. Crystal structures of the trimeric human immunodeficiency virus type 1 matrix protein: Implications for membrane association and assembly
35. 8+ lymphocytes respond to different HIV epitopes in seronegative and infected subjects
36. Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T lymphocyte responses
37. Prediction of proteasome cleavage motifs by neural networks
38. Mutational trends in V3 loop protein sequences observed in different genetic lineages of human immunodeficiency virus type 1
39. Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome
40. The determinants of HIV-1 protein evolution
41. Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody
42. Reduced susceptibility of human immunodeficiency virus type 1 (HIV-1) from patients with primary HIV infection to nonnucleoside reverse transcriptase inhibitors is associated with variation at novel amino acid sites
43. Immunogenic HIV variant peptides that bind to HLA-B8 can fail to stimulate cytotoxic T lymphocyte responses
44. Two novel T cell epitope prediction algorithms based on MHC-binding motifs: Comparison of predicted and published epitopes from Mycobacterium tuberculosis and HIV protein sequences
45. Cytotoxic-T-cell responses, viral load, and disease progression in early human immunodeficiency virus type 1 infection
46. The specificity of proteasomes: Impact on MHC class I processing and presentation of antigens
47. Identification of human immunodeficiency virus type 1 subtype c Gag-, Tat-, Rev-, and Nef-specific ELISPOT-based cytotoxic T-lymphocyte responses for AIDS vaccine design
48. Mechanisms of MHC class I-restricted antigen processing
49. Major expansion of CD8+ T cells with a predominant V beta usage during the primary immune response to HIV
50. How important is the 'quality' of the cytotoxic T lymphocyte (CTL) response in protection against HIV infection?
51. Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids
52. Control of viremia in simian immunodeficiency virus infection by CD8+ lymphocytes
53. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection
54. Helical interactions in the HIV-1 gp41 core reveal structural basis for the inhibitory activity of gp41 peptides
55. MHC class I antigen processing of an adenovirus CTL epitope is linked to the levels of immunoproteasomes in infected cells
56. Two new proteases in the MHC class I processing pathway
57. Discrete cleavage motifs of constitutive and immunoproteasomes revealed by quantitative analysis of cleavage products
58. Differential processing of class-I-restricted epitopes by the standard proteasome and the immunoproteasome
59. Molecular and functional analysis of a conserved CTL epitope in HIV-1 p24 recognized from a long-term nonprogressor: Constraints on immune escape associated with targeting a sequence essential for viral replication
60. Immune control of HIV: The obstacles of HLA and viral diversity
61. Frequent detection of escape from cytotoxic T-lymphocyte recognition in perinatal human immunodeficiency virus (HIV) type 1 transmission: The Ariel project for the prevention of transmission of HIV from mother to infant
62. Structure-based inhibitors of HIV-1 protease
63. The organization of human leucocyte antigen class I epitopes in HIV genome products: Implications for HIV evolution and vaccine design