data_5488
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
Backbone and 1H assignments for Tachyplesin I, phenylalanine mutant
;
_BMRB_accession_number 5488
_BMRB_flat_file_name bmr5488.str
_Entry_type original
_Submission_date 2002-08-02
_Accession_date 2002-08-02
_Entry_origination author
_NMR_STAR_version 2.1.1
_Experimental_method NMR
_Details .
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Laederach Alain . .
2 Andreotti Amy H .
3 Fulton Donald B .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 1
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 68
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2002-11-04 original author .
stop_
loop_
_Related_BMRB_accession_number
_Relationship
5486 'Tachyplesin I, Wild type'
5487 'Tachyplesin I, tyrosine mutant'
5489 'Tachyplesin I, alanine mutant'
stop_
_Original_release_date 2002-11-04
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title
;
Solution and micelle-bound structures of tachyplesin I and its active aromatic
linear derivatives
;
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID ?
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Laederach Alain . .
2 Andreotti Amy H .
3 Fulton Donald B .
stop_
_Journal_abbreviation Biochemistry
_Journal_volume 41
_Journal_issue .
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 12359
_Page_last 12368
_Year 2002
_Details .
loop_
_Keyword
'Tachyplesin I'
'beta hairpin'
'antimicrobial peptide'
dodecylphosphocholine
NMR
stop_
save_
#######################################
# Cited references within the entry #
#######################################
save_ref_1
_Saveframe_category citation
_Citation_full
;
Rao AG.
Conformation and antimicrobial activity of linear derivatives of tachyplesin
lacking disulfide bonds.
Arch Biochem Biophys. 1999 Jan 1;361(1):127-34.
;
_Citation_title 'Conformation and antimicrobial activity of linear derivatives of tachyplesin lacking disulfide bonds.'
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID 9882437
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Rao 'A G' G. .
stop_
_Journal_abbreviation 'Arch. Biochem. Biophys.'
_Journal_name_full 'Archives of biochemistry and biophysics'
_Journal_volume 361
_Journal_issue 1
_Journal_CSD .
_Book_title .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_publisher .
_Book_publisher_city .
_Book_ISBN .
_Conference_title .
_Conference_site .
_Conference_state_province .
_Conference_country .
_Conference_start_date .
_Conference_end_date .
_Conference_abstract_number .
_Thesis_institution .
_Thesis_institution_city .
_Thesis_institution_country .
_Page_first 127
_Page_last 134
_Year 1999
_Details
;
Tachyplesin is a potent antimicrobial peptide isolated from the hemocytes of the
horseshoe crab, Tachypleus tridentatus. Previous studies have shown that the
17-residue peptide has an intrinsic amphipathic structure conferred by two
antiparallel beta-sheets held rigidly by two disulfide bonds. Taking its short
length into account and the potential of such a small polypeptide to take on
multiple conformational states, one may assume that the disulfide bonds are
relevant determinants of function. However, in order to gain a global
perspective on the tolerance of cysteine residues in tachyplesin to amino acid
substitutions, a series of linear peptides have been synthesized and their
physicochemical properties analyzed. In these linear peptides, the cysteines
have been replaced with amino acids possessing different side-chain properties,
i.e., aliphatic hydrophobic (Ala, Leu, Ile, Val, and Met), aromatic hydrophobic
(Phe and Tyr), and acidic (Asp). Activity assays using natural and synthetic
membranes, and conformational measurements, highlight the subtle influence and
variability of the amino acid side-chain properties on peptide structure. While
an unequivocal interpretation of the results will have to await more refined
structural measurements, our results indicate that a rigidly held
disulfide-bonded beta-pleated sheet structure may not be absolutely essential
for antimicrobial activity. Furthermore, the results challenge the accepted
dogma of structure-activity relationships among antimicrobial peptides and
suggest that the maintenance of peptide hydrophobic-hydrophilic balance may be
a critical parameter, in addition to structure, in the design of peptides with
pharmaceutical relevance.
;
save_
save_ref_2
_Saveframe_category citation
_Citation_full
;
Tamamura H, Kuroda M, Masuda M, Otaka A, Funakoshi S, Nakashima H, Yamamoto N,
Waki M, Matsumoto A, Lancelin JM, et al.
A comparative study of the solution structures of tachyplesin I and a novel
anti-HIV synthetic peptide, T22 ([Tyr5,12, Lys7]-polyphemusin II), determined
by nuclear magnetic resonance.
Biochim Biophys Acta. 1993 May 13;1163(2):209-16.
;
_Citation_title 'A comparative study of the solution structures of tachyplesin I and a novel anti-HIV synthetic peptide, T22 ([Tyr5,12, Lys7]-polyphemusin II), determined by nuclear magnetic resonance.'
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID 8490053
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Tamamura H . .
2 Kuroda M . .
3 Masuda M . .
4 Otaka A . .
5 Funakoshi S . .
6 Nakashima H . .
7 Yamamoto N . .
8 Waki M . .
9 Matsumoto A . .
10 Lancelin 'J M' M. .
stop_
_Journal_abbreviation 'Biochim. Biophys. Acta'
_Journal_name_full 'Biochimica et biophysica acta'
_Journal_volume 1163
_Journal_issue 2
_Journal_CSD .
_Book_title .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_publisher .
_Book_publisher_city .
_Book_ISBN .
_Conference_title .
_Conference_site .
_Conference_state_province .
_Conference_country .
_Conference_start_date .
_Conference_end_date .
_Conference_abstract_number .
_Thesis_institution .
_Thesis_institution_city .
_Thesis_institution_country .
_Page_first 209
_Page_last 216
_Year 1993
_Details
;
The solution structure of tachyplesin I, which was isolated from membrane acid
extracts of the hemocytes from the Japanese horseshoe crab (Tachypleus
tridentatus), was determined by nuclear magnetic resonance (NMR) and distance
geometry calculation. Tachyplesin I takes an antiparallel beta-sheet structure
with a type-II beta-turn. Recently, among more than 20 synthetic peptides
associated with tachyplesin and its isopeptide (polyphemusin), we found that a
novel compound, which we designated as T22 ([Tyr5,12, Lys7]-polyphemusin II),
strongly inhibited the human immunodeficiency virus (HIV)-1-induced cytopathic
effect and viral antigen expression. The solution structure of T22 was
investigated using NMR, and its secondary structure was confirmed to be similar
to that of tachyplesin I. The anti-parallel beta-sheet structure and the
several amino-acid side chains on the plane of the beta-sheet of T22 are
thought to be associated with the expression of anti-HIV activity.
;
save_
##################################
# Molecular system description #
##################################
save_system_TP
_Saveframe_category molecular_system
_Mol_system_name 'Tachyplesin I, phenylalanine mutant'
_Abbreviation_common TP
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
'Tachyplesin I, phenylalanine mutant' $TP
stop_
_System_molecular_weight .
_System_physical_state native
_System_oligomer_state Monomer
_System_paramagnetic no
_System_thiol_state 'not present'
loop_
_Biological_function
'antimicrobial peptide'
stop_
_Database_query_date .
_Details 'Solution structures were not computed for TPF4 and TPA4.'
save_
########################
# Monomeric polymers #
########################
save_TP
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class protein
_Name_common 'Tachyplesin I, phenylalanine mutant'
_Abbreviation_common TP
_Molecular_mass .
_Mol_thiol_state 'not present'
_Details
;
Wild type, has two disulfide bridges (C3-C16, and C7-C12).
Wild Type, TPY4 and TPF4 adopt beta-hairpins.
TPY4, TPF4 and TPA4 are mutants in which the four Cyteine residues are
uniformly mutated to tyrosine, phenylalanine, and alanine, respectively.
;
##############################
# Polymer residue sequence #
##############################
_Residue_count 17
_Mol_residue_sequence KWFFRVFYRGIFYRRFR
loop_
_Residue_seq_code
_Residue_label
1 LYS 2 TRP 3 PHE 4 PHE 5 ARG
6 VAL 7 PHE 8 TYR 9 ARG 10 GLY
11 ILE 12 PHE 13 TYR 14 ARG 15 ARG
16 PHE 17 ARG
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date 2005-12-09
save_
####################
# Natural source #
####################
save_natural_source
_Saveframe_category natural_source
loop_
_Mol_label
_Organism_name_common
_NCBI_taxonomy_ID
_Superkingdom
_Kingdom
_Genus
_Species
_Details
$TP . . . . . . 'The peptide was synthetically produced and is not natural.'
stop_
save_
#########################
# Experimental source #
#########################
save_experimental_source
_Saveframe_category experimental_source
loop_
_Mol_label
_Production_method
_Host_organism_name_common
_Genus
_Species
_Strain
_Vector_name
$TP 'chemical synthesis' . . . . .
stop_
save_
#####################################
# Sample contents and methodology #
#####################################
########################
# Sample description #
########################
save_water_sample
_Saveframe_category sample
_Sample_type solution
_Details 'All experiments in water were done in these conditions.'
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Concentration_min_value
_Concentration_max_value
_Isotopic_labeling
$TP . mM 0.5 1.0 .
TFA 0.15 % . . .
stop_
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_NMR_spectrometer
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model DRX
_Field_strength 500
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_2D_1H-1H_NOESY_1
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H NOESY'
_Sample_label .
save_
save_2D_1H-1H_TOCSY_2
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H TOCSY'
_Sample_label .
save_
save_2D_1H-1H_ROESY_3
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H ROESY'
_Sample_label .
save_
save_NMR_spec_expt__0_1
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H NOESY'
_BMRB_pulse_sequence_accession_number .
_Details .
save_
save_NMR_spec_expt__0_2
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H TOCSY'
_BMRB_pulse_sequence_accession_number .
_Details .
save_
save_NMR_spec_expt__0_3
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H ROESY'
_BMRB_pulse_sequence_accession_number .
_Details .
save_
#######################
# Sample conditions #
#######################
save_condition_Water_25C
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
pH 3.0 0.2 n/a
temperature 298 1 K
'ionic strength' 0.0015 0.0001 %
stop_
save_
####################
# NMR parameters #
####################
##############################
# Assigned chemical shifts #
##############################
################################
# Chemical shift referencing #
################################
save_chemical_shift_reference
_Saveframe_category chemical_shift_reference
_Details .
loop_
_Mol_common_name
_Atom_type
_Atom_isotope_number
_Atom_group
_Chem_shift_units
_Chem_shift_value
_Reference_method
_Reference_type
_External_reference_sample_geometry
_External_reference_location
_External_reference_axis
_Indirect_shift_ratio
DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0
stop_
save_
###################################
# Assigned chemical shift lists #
###################################
###################################################################
# Chemical Shift Ambiguity Index Value Definitions #
# #
# The values other than 1 are used for those atoms with different #
# chemical shifts that cannot be assigned to stereospecific atoms #
# or to specific residues or chains. #
# #
# Index Value Definition #
# #
# 1 Unique (including isolated methyl protons, #
# geminal atoms, and geminal methyl #
# groups with identical chemical shifts) #
# (e.g. ILE HD11, HD12, HD13 protons) #
# 2 Ambiguity of geminal atoms or geminal methyl #
# proton groups (e.g. ASP HB2 and HB3 #
# protons, LEU CD1 and CD2 carbons, or #
# LEU HD11, HD12, HD13 and HD21, HD22, #
# HD23 methyl protons) #
# 3 Aromatic atoms on opposite sides of #
# symmetrical rings (e.g. TYR HE1 and HE2 #
# protons) #
# 4 Intraresidue ambiguities (e.g. LYS HG and #
# HD protons or TRP HZ2 and HZ3 protons) #
# 5 Interresidue ambiguities (LYS 12 vs. LYS 27) #
# 6 Intermolecular ambiguities (e.g. ASP 31 CA #
# in monomer 1 and ASP 31 CA in monomer 2 #
# of an asymmetrical homodimer, duplex #
# DNA assignments, or other assignments #
# that may apply to atoms in one or more #
# molecule in the molecular assembly) #
# 9 Ambiguous, specific ambiguity not defined #
# #
###################################################################
save_Shift_phenylalanine_mutant_in_water
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Sample_label
$water_sample
stop_
_Sample_conditions_label $condition_Water_25C
_Chem_shift_reference_set_label $chemical_shift_reference
_Mol_system_component_name 'Tachyplesin I, phenylalanine mutant'
_Text_data_format .
_Text_data .
loop_
_Atom_shift_assign_ID
_Residue_author_seq_code
_Residue_seq_code
_Residue_label
_Atom_name
_Atom_type
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code
1 . 1 LYS HA H 3.927 0.001 1
2 . 2 TRP H H 8.728 0.001 1
3 . 2 TRP HA H 4.636 0.001 1
4 . 2 TRP HB3 H 3.062 0.001 2
5 . 2 TRP HB2 H 3.143 0.001 2
6 . 3 PHE H H 8.035 0.001 1
7 . 3 PHE HA H 4.519 0.001 1
8 . 3 PHE HB3 H 2.737 0.001 2
9 . 3 PHE HB2 H 2.874 0.001 2
10 . 4 PHE H H 8.353 0.001 1
11 . 4 PHE HA H 4.423 0.001 1
12 . 4 PHE HB2 H 2.970 0.001 2
13 . 5 ARG H H 8.181 0.001 1
14 . 5 ARG HA H 4.333 0.001 1
15 . 5 ARG HB2 H 1.655 0.001 2
16 . 5 ARG HG3 H 1.467 0.001 2
17 . 5 ARG HG2 H 1.394 0.001 2
18 . 5 ARG HD2 H 3.019 0.001 2
19 . 6 VAL H H 8.361 0.001 1
20 . 6 VAL HA H 4.140 0.001 1
21 . 6 VAL HG2 H 0.809 0.001 4
22 . 6 VAL HG1 H 0.882 0.001 4
23 . 7 PHE H H 8.625 0.001 1
24 . 7 PHE HA H 4.731 0.001 1
25 . 7 PHE HB2 H 2.923 0.001 2
26 . 8 TYR H H 8.621 0.001 1
27 . 8 TYR HA H 4.512 0.001 1
28 . 8 TYR HB2 H 2.830 0.001 2
29 . 9 ARG H H 8.675 0.001 1
30 . 9 ARG HA H 3.936 0.001 1
31 . 9 ARG HB3 H 1.516 0.001 2
32 . 9 ARG HB2 H 1.760 0.001 2
33 . 9 ARG HG2 H 1.303 0.001 2
34 . 9 ARG HD2 H 2.827 0.001 2
35 . 10 GLY H H 7.587 0.001 1
36 . 10 GLY HA3 H 3.829 0.001 2
37 . 10 GLY HA2 H 3.972 0.001 2
38 . 11 ILE H H 7.807 0.001 1
39 . 11 ILE HA H 4.117 0.001 1
40 . 11 ILE HG12 H 1.284 0.001 4
41 . 11 ILE HG13 H 1.067 0.001 4
42 . 12 PHE H H 8.458 0.001 1
43 . 12 PHE HA H 4.705 0.001 1
44 . 12 PHE HB3 H 2.901 0.001 2
45 . 13 TYR H H 8.491 0.001 1
46 . 13 TYR HA H 4.473 0.001 1
47 . 13 TYR HB2 H 2.783 0.001 2
48 . 14 ARG H H 8.396 0.001 1
49 . 14 ARG HA H 4.214 0.001 1
50 . 14 ARG HB2 H 1.680 0.001 2
51 . 14 ARG HG2 H 1.541 0.001 2
52 . 14 ARG HD2 H 3.065 0.001 2
53 . 15 ARG H H 8.369 0.001 1
54 . 15 ARG HA H 4.332 0.001 1
55 . 15 ARG HB3 H 1.515 0.001 2
56 . 15 ARG HB2 H 1.635 0.001 2
57 . 15 ARG HG2 H 1.396 0.001 2
58 . 15 ARG HD2 H 3.039 0.001 2
59 . 16 PHE H H 8.528 0.001 1
60 . 16 PHE HA H 4.709 0.001 1
61 . 16 PHE HB3 H 2.899 0.001 2
62 . 16 PHE HB2 H 3.036 0.001 2
63 . 17 ARG H H 8.454 0.001 1
64 . 17 ARG HA H 4.240 0.001 1
65 . 17 ARG HB3 H 1.608 0.001 2
66 . 17 ARG HB2 H 1.773 0.001 2
67 . 17 ARG HG2 H 1.444 0.001 2
68 . 17 ARG HD2 H 3.001 0.001 2
stop_
loop_
_Atom_shift_assign_ID_ambiguity
22
'22,22,21,21,21'
'41,40'
stop_
save_