data_5613 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; A minimal beta-hairpin peptide scaffold for beta-turn display ; _BMRB_accession_number 5613 _BMRB_flat_file_name bmr5613.str _Entry_type original _Submission_date 2002-12-02 _Accession_date 2002-12-03 _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 Russell S. J. . 2 Blandl T. . . 3 Skelton N. J. . 4 Cochran A. G. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 62 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-16 update BMRB 'Updating non-standard residue' stop_ _Original_release_date 2002-12-03 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Stability of cyclic beta-hairins: asymmetric contributions from side chains of a hydrogen-bonded cross-strand residue pair ; _Citation_status 'in press' _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 Russell S. J. . 2 Blandl T. . . 3 Skelton N. J. . 4 Cochran A. G. . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . loop_ _Keyword 'beta hairpin' 'beta turn' 'cyclic disulfide' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_ref_1 _Saveframe_category citation _Citation_full ; Cochran AG, Tong RT, Starovasnik MA, Park EJ, McDowell RS, Theaker JE, Skelton NJ. A minimal peptide scaffold for beta-turn display: optimizing a strand position in disulfide-cyclized beta-hairpins. J Am Chem Soc. 2001 Jan 31;123(4):625-32. ; _Citation_title ; A minimal peptide scaffold for beta-turn display: optimizing a strand position in disulfide-cyclized beta-hairpins. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 11456574 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Cochran 'A. G.' G. . 2 Tong 'R. T.' T. . 3 Starovasnik 'M. A.' A. . 4 Park 'E. J.' J. . 5 McDowell 'R. S.' S. . 6 Theaker 'J. E.' E. . 7 Skelton 'N. J.' J. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 123 _Journal_issue 4 _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 625 _Page_last 632 _Year 2001 _Details ; Phage display of peptide libraries has become a powerful tool for the evolution of novel ligands that bind virtually any protein target. However, the rules governing conformational preferences in natural peptides are poorly understood, and consequently, structure-activity relationships in these molecules can be difficult to define. In an effort to simplify this process, we have investigated the structural stability of 10-residue, disulfide-constrained beta-hairpins and assessed their suitability as scaffolds for beta-turn display. Using disulfide formation as a probe, relative free energies of folding were measured for 19 peptides that differ at a one strand position. A tryptophan substitution promotes folding to a remarkable degree. NMR analysis confirms that the measured energies correlate well with the degree of beta-hairpin structure in the disulfide-cyclized peptides. Reexamination of a subset of the strand substitutions in peptides with different turn sequences reveals linear free energy relationships, indicating that turns and strand-strand interactions make independent, additive contributions to hairpin stability. Significantly, the tryptophan strand substitution is highly stabilizing with all turns tested, and peptides that display model turns or the less stable C'-C' ' turn of CD4 on this tryptophan "stem" are highly structured beta-hairpins in water. Thus, we have developed a small, structured beta-turn scaffold, containing only natural L-amino acids, that may be used to display peptide libraries of limited conformational diversity on phage. ; save_ ################################## # Molecular system description # ################################## save_system_bhpW _Saveframe_category molecular_system _Mol_system_name 'bhpW, disulfide cyclized beta-hairpin peptide' _Abbreviation_common bhpW _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label bhpW $bhpW stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_bhpW _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common bhpW _Abbreviation_common bhpW _Molecular_mass 1261 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence ; XCTWEGNKLTCX ; loop_ _Residue_seq_code _Residue_label 1 ACE 2 CYS 3 THR 4 TRP 5 GLU 6 GLY 7 ASN 8 LYS 9 LEU 10 THR 11 CYS 12 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_ACE _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'ACETYL GROUP' _BMRB_code . _PDB_code ACE _Standard_residue_derivative . _Molecular_mass 44.053 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Jul 25 16:20:39 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? O O O . 0 . ? CH3 CH3 C . 0 . ? H H H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 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 DOUB C O ? ? SING C CH3 ? ? SING C H ? ? SING CH3 H1 ? ? SING CH3 H2 ? ? SING CH3 H3 ? ? stop_ save_ 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 Mon Jul 25 11:50:28 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 _Details $bhpW . . . . . . Unclassified. 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 $bhpW 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $bhpW 5 mM . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 3.1 loop_ _Task collection stop_ _Details bruker save_ save_FELIX _Saveframe_category software _Name FELIX _Version 980 loop_ _Task 'data analysis' stop_ _Details bruker save_ save_DGII _Saveframe_category software _Name DGII _Version 980 loop_ _Task 'structure solution' stop_ _Details 'Tim Havel' save_ save_AMBER _Saveframe_category software _Name AMBER _Version 6.0 loop_ _Task refinement stop_ _Details 'Case, Kollman, ET. AL.' 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_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_2D_ROESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D ROESY' _Sample_label $sample_1 save_ save_2D_COSY-35_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D COSY-35' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0 0.01 M pH 5.0 0.1 n/a pressure 1 . atm temperature 288 1 K 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label DQF-COSY '2D TOCSY' '2D ROESY' '2D COSY-35' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name bhpW _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 ACE H21 H 2.06 0.02 1 2 . 2 CYS H H 8.47 0.02 1 3 . 2 CYS HA H 5.20 0.02 1 4 . 2 CYS HB2 H 3.05 0.02 1 5 . 2 CYS HB3 H 2.62 0.02 1 6 . 3 THR H H 8.86 0.02 1 7 . 3 THR HA H 4.55 0.02 1 8 . 3 THR HB H 4.14 0.02 1 9 . 3 THR HG2 H 1.17 0.02 1 10 . 4 TRP H H 8.71 0.02 1 11 . 4 TRP HA H 4.90 0.02 1 12 . 4 TRP HB2 H 3.26 0.02 2 13 . 4 TRP HB3 H 3.06 0.02 2 14 . 4 TRP HD1 H 7.22 0.02 1 15 . 4 TRP HE1 H 10.10 0.02 1 16 . 4 TRP HE3 H 7.34 0.02 1 17 . 4 TRP HZ2 H 7.43 0.02 1 18 . 4 TRP HZ3 H 6.97 0.02 1 19 . 4 TRP HH2 H 7.17 0.02 1 20 . 5 GLU H H 8.77 0.02 1 21 . 5 GLU HA H 4.54 0.02 1 22 . 5 GLU HB2 H 2.01 0.02 2 23 . 5 GLU HB3 H 1.93 0.02 2 24 . 5 GLU HG2 H 2.21 0.02 1 25 . 5 GLU HG3 H 2.21 0.02 1 26 . 6 GLY H H 8.88 0.02 1 27 . 6 GLY HA2 H 3.96 0.02 2 28 . 6 GLY HA3 H 3.71 0.02 2 29 . 7 ASN H H 8.65 0.02 1 30 . 7 ASN HA H 4.69 0.02 1 31 . 7 ASN HB2 H 2.95 0.02 1 32 . 7 ASN HB3 H 2.95 0.02 1 33 . 7 ASN HD21 H 7.61 0.02 1 34 . 7 ASN HD22 H 6.93 0.02 1 35 . 8 LYS H H 7.82 0.02 1 36 . 8 LYS HA H 4.52 0.02 1 37 . 8 LYS HB2 H 1.85 0.02 2 38 . 8 LYS HB3 H 1.77 0.02 2 39 . 8 LYS HG2 H 1.35 0.02 1 40 . 8 LYS HG3 H 1.35 0.02 1 41 . 8 LYS HD2 H 1.66 0.02 1 42 . 8 LYS HD3 H 1.66 0.02 1 43 . 8 LYS HE2 H 2.99 0.02 1 44 . 8 LYS HE3 H 2.99 0.02 1 45 . 8 LYS HZ H 7.55 0.10 1 46 . 9 LEU H H 8.47 0.02 1 47 . 9 LEU HA H 4.10 0.02 1 48 . 9 LEU HB2 H 1.39 0.02 2 49 . 9 LEU HB3 H 0.50 0.02 2 50 . 9 LEU HG H 1.05 0.02 1 51 . 9 LEU HD1 H 0.58 0.02 2 52 . 9 LEU HD2 H 0.11 0.02 2 53 . 10 THR H H 8.86 0.02 1 54 . 10 THR HA H 4.45 0.02 1 55 . 10 THR HB H 4.07 0.02 1 56 . 10 THR HG2 H 1.16 0.02 1 57 . 11 CYS H H 8.82 0.02 1 58 . 11 CYS HA H 5.00 0.02 1 59 . 11 CYS HB2 H 2.91 0.02 1 60 . 11 CYS HB3 H 3.07 0.02 1 61 . 12 NH2 HN1 H 7.57 0.02 2 62 . 12 NH2 HN2 H 7.26 0.02 2 stop_ save_