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_