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ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures.
(2005) Nucleic Acids Res 33
PubMed: 15980475 | PubMedCentral: PMC1160131 | DOI: 10.1093/nar/gki370
The run was carried out using PDB code 1bl8 ( 11 ) and default ConSurf parameters.
Publication Year: 2005
CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology.
PubMed: 15980521 | PubMedCentral: PMC1160177 | DOI: 10.1093/nar/gki416
The first example explains the usage of CAMPO in a well-studied case, the potassium channel from Streptomyces lividans (Kcsa, PDB code 1BL8), and its performance compared with ConSurf ( 20 ), one of t... e most commonly used servers for the identification of functionally important regions and ECRs.
The potassium channel from S.lividans To demonstrate the ability of CAMPO to detect evolutionarily conserved patches that are likely to be required for protein activity and stability, we report as example the analysis carried out on the potassium channel from S.lividans (Kcsa, PDB code 1BL8), a well-studied protein for which suitable sequence and structural information is known, and regions of functional importance have already been determined.
Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach.
(2006) BMC Bioinformatics 7
PubMed: 16836758 | PubMedCentral: PMC1590055 | DOI: 10.1186/1471-2105-7-340
Structures f C α -RMSD i BtuCD 1L7V 3.2 Dimer a A-Bs1678 g 0.63 BRD* 1BRR 2.9 Trimer b A-Bs162-Cs14 1.04 AmtB 1U77 1.35 Trimer a A-Bs7-Cs1 1.17 b A-Bs7-Cs1 0.83 c A-Bs1-Cs1 0.75 AcrB 1IWG 3.5 ... rimer a A-Bs4-Cs1 2.78 b A-Bs4-Cs1 1.56 c A-Bs1-Cs1 1.64 KcsA* 1BL8 3.3 Tetramer a A-Bs1-Cs500-Ds2 h 1.79 b A-Bs1-Cs1-Ds2 2.45 c A-Bs2-Cs1-Ds2 2.77 AQP1 1J4N 2.2 Tetramer a A-Bs2-Cs1-Ds1 1.31 b A-Bs1-Cs2-Ds1 1.71 c A-Bs2-Cs4-Ds1 1.37 GlpF 1FX8 2.2 Tetramer a A-Bs2-Cs1-Ds1 1.11 b A-Bs1-Cs2-Ds1 1.16 c A-Bs2-Cs2-Ds1 1.39 KirBac1 1P7B 3.65 Tetramer a A-Bs3-Cs1-Ds1 1.53 b A-Bs3-Cs1-Ds3 1.47 c A-Bs2-Cs1-Ds1 1.80 MscL* 1MSL 3.5 Pentamer a A-Bs5-Cs1-Ds4-Es6 3.45 b A-Bs5-Cs3-Ds2-Es1 2.83 c A-Bs8-Cs1-Ds1-Es6 2.47 MscS* 1MXM 3.9 Eptamer a A-Bs3-Cs3-Ds3-Es1-Fs1-Gs1 2.21 b A-Bs3-Cs3-Ds1-Es165-Fs3-Gs1 11.30 c A-Bs3-Cs1-Ds1-Es6-Fs1-Gs1 2.06 a Abbreviated name of the membrane proteins subjected to the benchmarks.
Benchmarks of the approach were first carried out on the tetrameric KcsA potassium channel H + gated (384 amino acids, PDB code: 1BL8 ; Figure 2 ) [ 25 ], pentameric MscL and eptameric MscS mechanosensitive channels (540 amino acids, PDB code: 1MSL , Figure 3 [ 26 ], and 1771 amino acids, PDB code: 1MXM , Figure 4 ) [ 27 ], respectively), and trimeric BRD (698 amino acids, PDB code: 1BRR ; Figure 5 ) [ 2 ].
Publication Year: 2006
A cation-pi interaction between extracellular TEA and an aromatic residue in potassium channels.
(2006) J Gen Physiol 128
PubMed: 17130518 | PubMedCentral: PMC2151593 | DOI: 10.1085/jgp.200609654
As noted, previous simulations were based on the analysis of two edge-on crystallographic structures (1BL8 and 2BOC) of the bacterial channel KcsA rather than on a eukaryotic voltage-gated potassium c... annel or on the en face structure of a KcsA mutant (2ATK).
Specifically, the side chain of Tyr82 in many published structures of KcsA (e.g., 1BL8 [ Doyle et al., 1998 ], 1K4C [ Zhou et al., 2001 ], 1R3J [ Zhou and MacKinnon, 2003 ], 2A9H [ Yu et al., 2005 ], and 1ZWI [ Cordero-Morales et al., 2006 ]; in the Protein Data Bank [ www.rcsb.org/pdb/ ]) is aligned such that a TEA positioned to block the channel would not interact with the face of the aromatic ring ( Fig. 1 , blue side chains).
Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels.
(2007) J Gen Physiol 129
PubMed: 17227917 | PubMedCentral: PMC2154357 | DOI: 10.1085/jgp.200609633
TABLE I Calculated ΔΔG (in kcal/mol) for the Binding Sites of KcsA and NaK Site KcsA (1K4C) KcsA (1BL8) NaK S0 −1.3 −1.1 S1 2.6 (2.1) 2.8 S2 5.3 (4.8) 6.6 −0.9 ... −1.1) S3 1.8 (2.7) 2.4 1.1 (1.7) S4 −1.2 −1.5 −0.9 Cavity −0.8 −0.2 −0.6 The calculations on the KcsA channel were done for the x-ray structures 1K4C ( Noskov et al., 2004 ) and 1BL8 ( Bernèche and Roux, 2001 ) using the CHARMM PARAM27 force field ( MacKerell et al., 1998 ).
Publication Year: 2007
Extracellular sodium interacts with the HERG channel at an outer pore site.
(2002) J Gen Physiol 120
PubMed: 12356854 | PubMedCentral: PMC2229534 | DOI: null
Generating Structural Hypotheses Based on the KcsA Crystal Structure Fig. 13 , which illustrates a putative structural effect of the S624A mutation, was created using the KcsA crystal structure coordi... ates, accession code 1BL8 ( Doyle et al., 1998 ) and Insight II modeling software (Molecular Simulations, Inc.) on a Silicon Graphics O 2 workstation.
Publication Year: 2002
Permeation of large tetra-alkylammonium cations through mutant and wild-type voltage-gated sodium channels as revealed by relief of block at high voltage.
(2000) J Gen Physiol 115
PubMed: 10736311 | PubMedCentral: PMC2233758 | DOI: null
This figure was prepared with WebLab ViewerPro software from Molecular Simulations Inc. using a crystal structure of KcsA ( Doyle et al. 1998 ) taken from the Brookhaven protein data base (entry numbe... 1BL8).
Publication Year: 2000
Permeation properties of inward-rectifier potassium channels and their molecular determinants.
PubMed: 10736307 | PubMedCentral: PMC2233762 | DOI: null
The KcsA ribbon model was constructed from coordinates downloaded from the PDB database, structure 1BL8.
On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation.
(2004) J Gen Physiol 124
PubMed: 15572347 | PubMedCentral: PMC2234034 | DOI: 10.1085/jgp.200409111
Fig. 8 shows the potential profile calculated for the 3.2 Å PDB:1BL8 ( Doyle et al., 1998 ) and 2.0 Å PDB:1K4C ( Zhou et al., 2001 ) resolution KcsA potassium channel structures.
Potential energy profiles for the 3.2 Å resolution PDB:1BL8 (- -) and 2.0 Å resolution PDB:1K4C (—) KcsA potassium channel structures.
Publication Year: 2004
Transmembrane helix prediction using amino acid property features and latent semantic analysis.
(2008) BMC Bioinformatics 9 Suppl 1
PubMed: 18315857 | PubMedCentral: PMC2259405 | DOI: 10.1186/1471-2105-9-S1-S4
Figure 2 shows the predicted TM segments of the KcsA potassium channel (PDB ID 1BL8 , [ 14 ]), the aquaporins (represented by PDB ID 1FQY [ 15 ]) and the human immunodeficiency virus (HIV) envelope gl... coprotein gp41 (structure unknown).
Publication Year: 2008
A residue at the cytoplasmic entrance of BK-type channels regulating single-channel opening by its hydrophobicity.
(2008) Biophys J 94
PubMed: 18400952 | PubMedCentral: PMC2292367 | DOI: 10.1529/biophysj.107.120022
Modeling and MD simulations The homologous structure of the pore region of mSlo and I323T channels at the closed state was built using the structure of the KcsA channel (PDB code: 1BL8) as a template ... hrough the SWISSMODEL server ( 31 ), based on their high sequence identity in the S5-P-S6 region, and additional 8-ns MD simulations were performed on the model to get a sufficiently equilibrated structure.
Cysteine mutagenesis and computer modeling of the S6 region of an intermediate conductance IKCa channel.
PubMed: 12084779 | PubMedCentral: PMC2311397 | DOI: null
Structural data for the closed KcsA channel were obtained from the protein data bank 1BL8 file.
A fully atomistic model of the Cx32 connexon.
(2008) PLoS One 3
PubMed: 18648547 | PubMedCentral: PMC2481295 | DOI: 10.1371/journal.pone.0002614
The reliability of this procedure was verified on the structure of the Potassium channel (KcsA) from Streptomyces Lividans , one of the best characterized ionic channels, solved by X-ray crystallograp... y (  , PDB entry code:1BL8).
Cooperative transition between open and closed conformations in potassium channels.
(2008) PLoS Comput Biol 4
PubMed: 18769593 | PubMedCentral: PMC2528004 | DOI: 10.1371/journal.pcbi.1000164
Materials and Methods Structures Three structures of the homotetrameric channel were used: two of KcsA (PDB identifiers: 1bl8  and 1k4c  ; Figure 1B ) and one of... MthK (PBB: 1lnq  ; Figure 2B ).
The upper panels show a side view of the X-ray crystal structure of the channel (B; PDB identifier 1bl8) and the slowest mode of fluctuations in opposite directions (A and C).
Results/Discussion We analyzed the two structures of the KcsA channel (PBD identifiers 1bl8  and 1k4c  ; Figure 1B and 1E ) and the structure of the MthK channel (PDB identifier 1lnq  ; Figure 2B and 2E ).
hERG gating microdomains defined by S6 mutagenesis and molecular modeling.
(2008) J Gen Physiol 132
PubMed: 18955593 | PubMedCentral: PMC2571969 | DOI: 10.1085/jgp.200810083
A model based on the Streptomyces lividans potassium channel (KcsA; PDB ID 1BL8) coordinates was also constructed and found to be in close agreement with the MlotiK1 model (see Supplemental Materials ... nd methods and Figs.
ProteinShader: illustrative rendering of macromolecules.
(2009) BMC Struct Biol 9
PubMed: 19331660 | PubMedCentral: PMC2672931 | DOI: 10.1186/1472-6807-9-19
PDB ID Residues Atoms Protein 1AQB 175 1574 retinol-binding protein 1BL8 388 2824 potassium channel 6ADH 748 5669 alcohol dehydrogenase 13PK 1660 12508 phosphoglycerate kinase 1E79 3315 25248 F1 ATPas... inhibited by DCCD 1AON 8015 59674 GroEL-GroES-(ADP)7 chaperonin complex The performance tests graphed in Figures 10 to 12 were made on a Macintosh 2.16 GHz Intel Core 2 Duo with 2 GB of RAM and an ATI Radeon X1600 graphics card with 256 MB VRAM.
(D) The potassium channel [PDB: 1BL8 ], a transmembrane α-domain structure [ 32 ], with a K+ ion (deep pink) in the channel.
Publication Year: 2009
Mechanism of differential control of NMDA receptor activity by NR2 subunits.
(2009) Nature 459
PubMed: 19404260 | PubMedCentral: PMC2711440 | DOI: 10.1038/nature07993
Construction of Figure 4 The molecular architecture shown in figure 4a was illustrated by the crystal structure of the mGluR1 ligand-binding domain dimer (pdb 1ewv, ref 37 ) at the level of the NTD, t... e NMDAR NR1/NR2A agonist-binding domain dimer (pdb 2a5T, ref 30 ) and two subunits of the KcsA tetramer (pdb 1bl8, ref 38 ) as the transmembrane region of the receptor.
Molecular endpoints of Ca2+/calmodulin- and voltage-dependent inactivation of Ca(v)1.3 channels.
(2010) J Gen Physiol 135
PubMed: 20142517 | PubMedCentral: PMC2828906 | DOI: 10.1085/jgp.200910308
1BL8 ) crystal structure was used as template ( Doyle et al., 1998 ).
Publication Year: 2010
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