data_5941 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Proton chemical shift assignments for cycloCP-11 ; _BMRB_accession_number 5941 _BMRB_flat_file_name bmr5941.str _Entry_type original _Submission_date 2003-09-09 _Accession_date 2003-09-09 _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 Rozek Annett . . 2 Powers Jon-Paul S. . 3 Friedrich Carol L. . 4 Hancock Robert E.W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 128 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-17 update BMRB 'Updating non-standard residue' stop_ loop_ _Related_BMRB_accession_number _Relationship 4552 'The proton chemical shifts for the native parent peptide indolicidin' 5938 'CP-11in DPC micelles' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure-based design of an indolicidin peptide analogue with increased protease stability ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 14640680 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Rozek Annet . . 2 Powers Jon-Paul S. . 3 Friedrich Carol L. . 4 Hancock Robert E.W. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 42 _Journal_issue 48 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 14130 _Page_last 14138 _Year 2003 _Details . loop_ _Keyword 'antimicrobial cationic peptide' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_reference_1 _Saveframe_category citation _Citation_full ; Rozek A, Friedrich CL, Hancock RE. Biochemistry. 2000 Dec 26;39(51):15765-74. ; _Citation_title 'Structure of the bovine antimicrobial peptide indolicidin bound to dodecylphosphocholine and sodium dodecyl sulfate micelles.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 11123901 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Rozek A. . . 2 Friedrich C.L. L. . 3 Hancock R.E. E. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 39 _Journal_issue 51 _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 15765 _Page_last 15774 _Year 2000 _Details ; Indolicidin is a cationic, 13-residue antimicrobial peptide (ILPWKWPWWPWRR-NH(2)) which is unusually rich in tryptophan and proline. Its antimicrobial action involves the bacterial cytoplasmic membrane. Fluorescence and circular dichroism spectra demonstrated the structural similarity of indolicidin in complexes with large unilamellar phospolipid vesicles and with detergent micelles. The structure of indolicidin bound to zwitterionic dodecylphosphocholine (DPC) and anionic sodium dodecyl sulfate (SDS) micelles was determined using NMR methods and shown to represent a unique membrane-associated peptide structure. The backbone structure in DPC, well defined between residues 3 and 11, was extended, with two half-turns at residues Lys-5 and Trp-8. The backbone structure in SDS, well defined between residues 5 and 11, was also extended, but lacked the bend in the C-terminal half. Indolicidin in complexes with DPC had a central hydrophobic core composed of proline and tryptophan, which was bracketed by positively charged regions near the peptide termini. The tryptophan side chains, with one exception, folded flat against the peptide backbone, thus giving the molecule a wedge shape. Indolicidin in complexes with SDS had an arrangement of hydrophobic and cationic regions similar to that found in the presence of DPC. The tryptophan side chains were less well defined than for indolicidin in DPC and extended away from the peptide backbone. The preferred location of indolicidin in DPC micelles and lipid bilayers, analyzed using spin-label probes, was at the membrane interface. ; save_ ################################## # Molecular system description # ################################## save_cycloCP-11 _Saveframe_category molecular_system _Mol_system_name 'cycloCP-11in DPC micelles' _Abbreviation_common cycloCP-11 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'cycloCP-11 monomer' $indolicidin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' loop_ _Biological_function 'antimicrobial peptide' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_indolicidin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common indolicidin _Name_variant cycloCP-11 _Abbreviation_common indolicidin _Molecular_mass 2084 _Mol_thiol_state 'all disulfide bound' _Details 'tryptophan and proline rich' ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence ICLKKWPWWPWRRCKX loop_ _Residue_seq_code _Residue_label 1 ILE 2 CYS 3 LEU 4 LYS 5 LYS 6 TRP 7 PRO 8 TRP 9 TRP 10 PRO 11 TRP 12 ARG 13 ARG 14 CYS 15 LYS 16 NH2 stop_ _Sequence_homology_query_date 2005-11-24 _Sequence_homology_query_revised_last_date 2005-11-22 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 5938 indolicidin 115.38 13 100 100 0.32 BMRB 5941 indolicidin 100.00 15 100 100 0.001 PDB 1G89 'A Chain A, Structure Of The BovineAntimicrobial Peptide Indolicidin Bound ToDodecylphosphocholine Micelles' 107.14 14 100 100 3.5 PDB 1G8C 'A Chain A, Structure Of The BovineAntimicrobial Peptide Indolicidin Bound To SodiumDodecyl Sulfate Micelles' 107.14 14 100 100 3.5 PDB 1QXQ 'A Chain A, Structure Of An IndolicidinPeptide Derivative With Higher Charge' 107.14 14 100 100 0.32 PDB 1QX9 'A Chain A, Structure Of A Cyclic IndolicidinPeptide Derivative With Higher Charge' 93.75 16 100 100 0.001 EMBL CAA47755.1 'cathelicidin [Bos taurus]' 10.42 144 100 100 3.5 GenBank AAB21494.1 'indolicidin=antimicrobial peptide[cattle, neutrophils, Peptide, 13 aa]' 115.38 13 100 100 3.5 REF NP_777252.1 'cathelicidin 4 [indolicidin] [Bostaurus]' 10.42 144 100 100 3.5 SWISS-PROT P33046 'INDC_BOVIN Indolicidin precursor' 10.42 144 100 100 3.5 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'AMINO GROUP' _BMRB_code . _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Jul 20 11:58:19 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N HN1 ? ? SING N HN2 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $indolicidin cow 9913 Eukaryota Metazoa Bos taurus 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 _Details $indolicidin 'chemical synthesis' . . . . . 'FMOC-based solid phase synthesis' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type micelles _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $indolicidin 2 mM . DPC 200 mM . stop_ save_ ############################ # Computer software used # ############################ save_NMRPIPE _Saveframe_category software _Name NMRPIPE _Version 2002 loop_ _Task processing stop_ _Details 'Frank Delaglio, NIH' save_ save_NMRVIEW _Saveframe_category software _Name NMRVIEW _Version 5.0.4 loop_ _Task analysis stop_ _Details 'Bruce Johnson, Merck' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Inova _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_Ex-cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.6 0.2 n/a temperature 310 1 K 'ionic strength' 202 . mM pressure 1 . atm 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 H2O H 1 H ppm 4.60 internal direct spherical internal parallel 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_set_1 _Saveframe_category assigned_chemical_shifts _Details ; Several unassigned signals were observed that may correspond to a minor conformational species ; loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $Ex-cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'cycloCP-11 monomer' _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 ILE HA H 3.86 0.01 1 2 . 1 ILE HB H 1.92 0.01 1 3 . 1 ILE HG12 H 1.51 0.01 2 4 . 1 ILE HG13 H 1.12 0.01 2 5 . 1 ILE HG2 H 0.90 0.01 1 6 . 1 ILE HD1 H 0.84 0.01 1 7 . 2 CYS H H 8.80 0.01 1 8 . 2 CYS HA H 4.95 0.01 1 9 . 2 CYS HB2 H 2.93 0.01 2 10 . 2 CYS HB3 H 3.00 0.01 2 11 . 3 LEU H H 8.01 0.01 1 12 . 3 LEU HA H 4.25 0.01 1 13 . 3 LEU HB2 H 1.26 0.01 2 14 . 3 LEU HB3 H 1.08 0.01 2 15 . 3 LEU HG H 1.18 0.01 1 16 . 3 LEU HD1 H 0.44 0.01 2 17 . 3 LEU HD2 H 0.38 0.01 2 18 . 4 LYS H H 8.01 0.01 1 19 . 4 LYS HA H 4.08 0.01 1 20 . 4 LYS HB2 H 1.27 0.01 1 21 . 4 LYS HB3 H 1.27 0.01 1 22 . 4 LYS HG2 H 1.22 0.01 1 23 . 4 LYS HG3 H 1.22 0.01 1 24 . 4 LYS HD2 H 1.56 0.01 1 25 . 4 LYS HD3 H 1.56 0.01 1 26 . 4 LYS HE2 H 2.87 0.01 1 27 . 4 LYS HE3 H 2.87 0.01 1 28 . 4 LYS HZ H 7.47 0.01 1 29 . 5 LYS H H 7.78 0.01 1 30 . 5 LYS HA H 3.95 0.01 1 31 . 5 LYS HB2 H 1.28 0.01 1 32 . 5 LYS HB3 H 1.28 0.01 1 33 . 5 LYS HG2 H 0.87 0.01 1 34 . 5 LYS HG3 H 0.87 0.01 1 35 . 5 LYS HD2 H 1.30 0.01 1 36 . 5 LYS HD3 H 1.30 0.01 1 37 . 5 LYS HE2 H 2.64 0.01 1 38 . 5 LYS HE3 H 2.64 0.01 1 39 . 5 LYS HZ H 7.54 0.01 2 40 . 6 TRP H H 7.69 0.01 1 41 . 6 TRP HA H 4.76 0.01 1 42 . 6 TRP HB2 H 2.74 0.01 2 43 . 6 TRP HB3 H 2.09 0.01 2 44 . 6 TRP HD1 H 7.26 0.01 1 45 . 6 TRP HE1 H 10.40 0.01 1 46 . 6 TRP HE3 H 7.13 0.01 1 47 . 6 TRP HZ2 H 7.35 0.01 1 48 . 6 TRP HZ3 H 6.75 0.01 1 49 . 6 TRP HH2 H 6.98 0.01 1 50 . 7 PRO HA H 4.21 0.01 1 51 . 7 PRO HB2 H 1.78 0.01 2 52 . 7 PRO HB3 H 2.19 0.01 2 53 . 7 PRO HG2 H 1.88 0.01 2 54 . 7 PRO HG3 H 1.96 0.01 2 55 . 7 PRO HD2 H 3.65 0.01 2 56 . 7 PRO HD3 H 3.82 0.01 2 57 . 8 TRP H H 6.47 0.01 1 58 . 8 TRP HA H 4.37 0.01 1 59 . 8 TRP HB2 H 3.11 0.01 1 60 . 8 TRP HB3 H 3.11 0.01 1 61 . 8 TRP HD1 H 7.23 0.01 1 62 . 8 TRP HE1 H 10.47 0.01 1 63 . 8 TRP HE3 H 7.28 0.01 4 64 . 8 TRP HZ2 H 6.69 0.01 1 65 . 8 TRP HZ3 H 7.28 0.01 4 66 . 8 TRP HH2 H 6.91 0.01 1 67 . 9 TRP H H 7.36 0.01 1 68 . 9 TRP HA H 4.66 0.01 1 69 . 9 TRP HB2 H 2.95 0.01 2 70 . 9 TRP HB3 H 3.13 0.01 2 71 . 9 TRP HD1 H 7.14 0.01 1 72 . 9 TRP HE1 H 10.30 0.01 1 73 . 9 TRP HE3 H 7.65 0.01 1 74 . 9 TRP HZ2 H 7.52 0.01 1 75 . 9 TRP HZ3 H 7.17 0.01 1 76 . 9 TRP HH2 H 7.18 0.01 1 77 . 10 PRO HA H 4.12 0.01 1 78 . 10 PRO HB2 H 0.71 0.01 2 79 . 10 PRO HB3 H 1.63 0.01 2 80 . 10 PRO HG2 H 0.28 0.01 2 81 . 10 PRO HG3 H 1.12 0.01 2 82 . 10 PRO HD2 H 2.23 0.01 2 83 . 10 PRO HD3 H 3.57 0.01 2 84 . 11 TRP H H 5.78 0.01 1 85 . 11 TRP HA H 4.74 0.01 1 86 . 11 TRP HB2 H 2.91 0.01 2 87 . 11 TRP HB3 H 3.35 0.01 2 88 . 11 TRP HD1 H 7.18 0.01 1 89 . 11 TRP HE1 H 10.50 0.01 1 90 . 11 TRP HE3 H 6.48 0.01 1 91 . 11 TRP HZ2 H 7.24 0.01 1 92 . 11 TRP HZ3 H 6.39 0.01 1 93 . 11 TRP HH2 H 6.82 0.01 1 94 . 12 ARG H H 8.30 0.01 1 95 . 12 ARG HA H 4.31 0.01 1 96 . 12 ARG HB2 H 1.85 0.01 2 97 . 12 ARG HB3 H 1.96 0.01 2 98 . 12 ARG HG2 H 1.64 0.01 1 99 . 12 ARG HG3 H 1.64 0.01 1 100 . 12 ARG HD2 H 3.18 0.01 1 101 . 12 ARG HD3 H 3.18 0.01 1 102 . 12 ARG HE H 7.31 0.01 1 103 . 13 ARG H H 8.31 0.01 1 104 . 13 ARG HA H 4.47 0.01 1 105 . 13 ARG HB2 H 1.74 0.01 2 106 . 13 ARG HB3 H 1.89 0.01 2 107 . 13 ARG HG2 H 1.56 0.01 2 108 . 13 ARG HG3 H 1.66 0.01 2 109 . 13 ARG HD2 H 3.17 0.01 1 110 . 13 ARG HD3 H 3.17 0.01 1 111 . 13 ARG HE H 7.25 0.01 1 112 . 14 CYS H H 8.15 0.01 1 113 . 14 CYS HA H 4.83 0.01 1 114 . 14 CYS HB2 H 3.04 0.01 2 115 . 14 CYS HB3 H 3.18 0.01 2 116 . 15 LYS H H 8.41 0.01 1 117 . 15 LYS HA H 4.24 0.01 1 118 . 15 LYS HB2 H 1.64 0.01 2 119 . 15 LYS HB3 H 1.76 0.01 2 120 . 15 LYS HG2 H 1.39 0.01 2 121 . 15 LYS HG3 H 1.39 0.01 2 122 . 15 LYS HD2 H 1.63 0.01 2 123 . 15 LYS HD3 H 1.63 0.01 2 124 . 15 LYS HE2 H 2.91 0.01 2 125 . 15 LYS HE3 H 2.91 0.01 2 126 . 15 LYS HZ H 7.56 0.01 1 127 . 16 NH2 HN1 H 6.66 0.01 2 128 . 16 NH2 HN2 H 7.41 0.01 2 stop_ save_