Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 7

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Mechanosensitive channel MscS in the open state: modeling of the transition, explicit simulations, and experimental measurements of conductance.

(2008) J Gen Physiol 132

PubMed: 18591417 | PubMedCentral: PMC2442180 | DOI: 10.1085/jgp.200810000

This original crystal structure and the refined version (PDB ID 2OAU) are equally usable for explorations of the transmembrane part of the protein since substantial refinements involving registry shif... s took place only in the cytoplasmic “cage” domain.

This structure was recently replaced by the refined 2OAU structure ( Steinbacher et al., 2007 ).

Publication Year: 2008

Transmembrane protein topology prediction using support vector machines.

(2009) BMC Bioinformatics 10

PubMed: 19470175 | PubMedCentral: PMC2700806 | DOI: 10.1186/1471-2105-10-159

For example, OPM lists Mechanosensitive channel protein MscS (PDB: 2oau ) as having two TM helices, neither of which fully cross the membrane, whereas the PDB_TM definition of 3 TM helices appears mor... plausible.

Publication Year: 2009

PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.

(2009) PLoS Comput Biol 5

PubMed: 19609355 | PubMedCentral: PMC2704872 | DOI: 10.1371/journal.pcbi.1000440

(A) KirBac1.1 potassium channel (1p7b); (B) bovine aquaporin-1 (1j4n); (C) KcsA potassium channel (1k4c); (D) MthK calcium-gated potassium channel (1lnq); (E) CorA Mg 2+ transporter (2iub); (F... MscS voltage-modulated mechanosensitive channel (2oau); (G) ASIC1 acid-sensing ion channel (2qts); (H) SecYE-beta protein-conducting channel (2yxr); (I) Kv1.2 voltage-gated potassium channel (2a79); (J) sodium-potassium channel (2ahy); (K) Amt-1 ammonium channel (2b2f); (L) nicotinic acetylcholine receptor (2bg9).

(A)&(D) MthK potassium channel (1lnq), (B)&(E) MscS voltage-modulated mechanosensitive channel (2oau); (C)&(F) bovine aquaporin-0 (1ymg), (G)&(J) ASIC1 acid-sensing ion channel (2qts); (H)&(K) Amt-1 ammonium channel (2b2f); (I)&(L) SoPiP2;1 water channel (1z98).

Publication Year: 2009

Mechanobiology in cardiac physiology and diseases.

(2013) J Cell Mol Med 17

PubMed: 23441631 | PubMedCentral: PMC3822585 | DOI: 10.1111/jcmm.12027

( A ) Opening of the bacterial mechanosensitive channel of small conductance (MscS, PDB accession number: 2OAU) in response to lipid bilayer stretch obtained by coarse-grained molecular dynamics simul... tion.

Publication Year: 2013

Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices.

(2013) BMC Bioinformatics 14

PubMed: 24112406 | PubMedCentral: PMC3854514 | DOI: 10.1186/1471-2105-14-304

Table 7 The list of all protein chains (PDB:Chain) included in the development set and the independent test set Development set Independent test set 1E7P:C 1LNQ:A 1YCE:A 2 F93:A 2PNO:A 2WIT:A ... B8C:A 3EH4:A 2XQ2:A 3MP7:A 1EYS:L 1ORQ:C 1YEW:C 2GFP:A 2Q67:A 2WSW:A 3CHX:A 3EHB:B 2XUT:A 3NYM:A 1EYS:M 1P7B:A 1YQ3:C 2GIF:A 2Q7R:A 2YVX:A 3CHX:B 3G5U:A 3KBC:A 3O0R:B 1FFT:A 1PV6:A 1YQ3:D 2IUB:A 2QJY:A 2Z73:A 3CIR:C 3GIA:A 3KCU:A 3O7P:A 1FFT:B 1PW4:A 1ZCD:A 2JLO:A 2R6G:F 2ZD9:A 3CIR:D 3H90:A 3KG2:A 3OE6:A 1FFT:C 1QLE:C 2A65:A 2NMR:A 2R6G:G 2ZJS:Y 3CN5:A 3H9V:A 3KJ6:A 3ORG:A 1FX8:A 1S5L:B 2AXT:A 2NQ2:A 2R9R:B 2ZW3:A 3D31:C 3HD6:A 3KP9:A 3P4W:A 1GZM:A 1S5L:C 2AXT:D 2NR9:A 2VL0:A 2ZXE:A 3DDL:A 3IJ4:A 3L1L:A 3P5N:A 1JB0:K 1S5L:Z 2BL2:A 2OAR:A 2VPZ:C 3A7K:A 3DHW:A 3JYC:A 3 M71:A 3PJZ:A 1JV6:A 1XIO:A 2C3E:A 2OAU:A 2WDV:C 3B4R:A 3E9J:C 3 K07:A 3MK7:A   1KPK:A 1Y4Z:C 2E75:B 2ONJ:A 2WDV:D 3B5D:A 3EFF:K 3K3F:A 3MK7:C   1KQG:C               3MKT:A   Calculation of relative accessible surface area from structures To calculate lipid exposure or exposed area of a structure, we used NACCESS program [ 19 , 29 ] with the probe radius set to 2.0 Å.

Publication Year: 2013

The cytoplasmic cage domain of the mechanosensitive channel MscS is a sensor of macromolecular crowding.

(2014) J Gen Physiol 143

PubMed: 24778428 | PubMedCentral: PMC4003192 | DOI: 10.1085/jgp.201311114

Examination of the WT MscS crystal structure (PDB ID 2OAU [ Steinbacher et al., 2007 ]) obtained in foscholine (in the absence of lipids) suggests that its conformation resembles a nonconductive inact... vated state ( Sukharev et al., 2007 ).

MATERIALS AND METHODS Modeling and simulations We used the extrapolated motion protocol ( Akitake et al., 2007 ; Anishkin et al., 2008b ) to generate a set of nonrandom models from the crystal structure of WT MscS (PDB ID 2OAU [ Steinbacher et al., 2007 ]).

The model of the inactivated state resembles the crystal conformation (PDB ID 2OAU ); however, the splay of the peripheral TM1 and TM2 helices (ocher and green) is less.

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4519979

The anisotropy data were fitted using the C β –C β distances of the same residue in neighboring subunits obtained from the closed and open structures (PDB entries 2oau and 2vv5... respectively) assuming a FRET mechanism.

In the closed crystal structure [Protein Data Bank (PDB) entry 2OAU], V99 is exposed in the crevice between TM1/TM2 and TM3a, which could accommodate the increased volume of Trp (∼50% increase relative to that of Val).

The high conductance may be explained by a π–π interaction between V99W and F80 on adjacent subunits (i.e., V99W:a with F80A:b) in the open state (B; PDB entry 2VV5), whereas the residues are well-separated in the closed state (C; PDB entry 2OAU) (V99W is colored red and F80 green).

The figures were generated with PyMol on the basis of the closed crystal structure (PDB entry 2OAU).

Distances of C β atoms from neighboring subunits were obtained from the closed crystal structure (PDB entry 2OAU), and means and standard deviations are given for the distances in the asymmetric complex.

b values for C β atoms from the closed structure are given or, in the case of glycines, for C α atoms (PDB entry 2OAU).

(B) The positions of the residues are shown on the closed structure 2OAU.

The residues in TM1 (N30) and TM2 (R88) are adjacent in the crystal structure (Figure S5 of the Supporting Information ) and are predicted to form a H-bond (see the OCA database for 2oau).

In the MscS crystal structure (Protein Data Bank entry 2oau), a narrow, hydrophobic opening is visible in the crystal structure, and it has been proposed that a vapor lock created by the hydrophobic seals, L105 and L109, is the barrier to water and ions.

Publication Year: 2015