The protein data bank: A computer-based archival file for macromolecular structures

Bernstein, F.C.; Koetzle, Thomas F.; Williams, G. J. B.; Meyer, Edgar F.; Brice, Michael D.; Rodgers, John R.; Kennard, Olga; Shimanouchi, Takehiko; Tasumi, Mitsuo

doi:10.1016/0003-9861(78)90204-7

Cited by 1,128 publications

(1,208 citation statements)

References 8 publications

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“…Finally the model was saved and exported in the PDB file format. 56 The size of HRP was evaluated from the PDB file number 1HCH using the VMD program. 57 MD Simulations of Cage hp (3T).…”

Section: Methodsmentioning

confidence: 99%

Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage

et al. 2013

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We demonstrate temperature-controlled encapsulation and release of the enzyme horseradish peroxidase using a preassembled and covalently closed three-dimensional DNA cage structure as a controllable encapsulation device. The utilized cage structure was covalently closed and composed of 12 double-stranded B-DNA helices that constituted the edges of the structure. The double stranded helices were interrupted by short single-stranded thymidine linkers constituting the cage corners except for one, which was composed by four 32 nucleotide long stretches of DNA with a sequence that allowed them to fold into hairpin structures. As demonstrated by gel-electrophoretic and fluorophore-quenching experiments this design imposed a temperature-controlled conformational transition capability to the structure, which allowed entrance or release of an enzyme cargo at 37 °C while ensuring retainment of the cargo in the central cavity of the cage at 4 °C. The entrapped enzyme was catalytically active inside the DNA cage and was able to convert substrate molecules penetrating the apertures in the DNA lattice that surrounded the central cavity of the cage.

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“…Finally the model was saved and exported in the PDB file format. 56 The size of HRP was evaluated from the PDB file number 1HCH using the VMD program. 57 MD Simulations of Cage hp (3T).…”

Section: Methodsmentioning

confidence: 99%

Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage

et al. 2013

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“…The AChE crystal structure with PDB code 2CKM from the RCSB Protein Data Bank was selected for this purpose. 31,33 It corresponds to the structure of Torpedo californica AChE (TcAChE) in complex with a bis-tacrine linked by a seven-carbon spacer. The selection was based on the good resolution of the structure (2.15 Å) and the similarity of the bound ligand with the compounds investigated here.…”

Section: ■ Methodsmentioning

confidence: 99%

Acetylcholinesterase Inhibitors with Photoswitchable Inhibition of β-Amyloid Aggregation

Chen

Wehle

Kuzmanovic³

et al. 2014

ACS Chem. Neurosci.

102

103

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Photochromic cholinesterase inhibitors were obtained from cis-1,2-α-dithienylethene-based compounds by incorporating one or two aminopolymethylene tacrine groups. All target compounds are potent acetyl-(AChE) and butyrylcholinesterase (BChE) inhibitors in the nanomolar concentration range. Compound 11b bearing an octylene linker exhibited interactions with both the catalytic active site (CAS) and the peripheral anionic site (PAS) of AChE. Yet upon irradiation with light, the mechanism of interaction varied from one photochromic form to another, which was investigated by kinetic studies and proved "photoswitchable". The AChE-induced β-amyloid (Aβ) aggregation assay gave further experimental support to this finding: Aβ 1−40 aggregation catalyzed by the PAS of AChE might be inhibited by compound 11b in a concentration-dependent manner and seems to occur only with one photochromic form. Computational docking studies provided potential binding modes of the compound. Docking studies and molecular dynamics (MD) simulations for the ringopen and -closed form indicate a difference in binding. Although both forms can interact with the PAS, more stable interactions are observed for the ring-open form based upon stabilization of a water molecule network within the enzyme, whereas the ringclosed form lacks the required conformational flexibility for an analogous binding mode. The photoswitchable inhibitor identified might serve as valuable molecular tool to investigate the different biological properties of AChE as well as its role in pathogenesis of AD in in vitro assays.

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“…This method is limited, however, to cases where the primary structures of the aligned proteins are homologous. Because the primary sequences of most proteins are not homologous to those of any protein of known structure in the Brookhaven Protein Data Bank (PDB) (Bernstein et al, 1977), a method that is independent of the knowledge of the three-dimensional structure is desirable.…”

Section: ~~~mentioning

confidence: 99%

Paired natural cysteine mutation mapping: Aid to constraining models of protein tertiary structure

1995

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This paper discusses the benefit of mapping paired cysteine mutation patterns as a guide to identifying the positions of protein disulfide bonds. This information can facilitate the computer modeling of protein tertiary structure. First, a simple, paired natural-cysteine-mutation map is presented that identifies the positions of putative disulfide bonds in protein families. The method is based on the observation that if, during the process of evolution, a disulfide-bonded cysteine residue is not conserved, then it is likely that its counterpart will also be mutated. For each target protein, protein databases were searched for the primary amino acid sequences of all known members of distinct protein families. Primary sequence alignment was carried out using Pileup algorithms in the GCG package. To search for correlated mutations, we listed only the positions where cysteine residues were highly conserved and emphasized the mutated residues. In proteins of known three-dimensional structure, a striking pattern of paired cysteine mutations correlated with the positions of known disulfide bridges. For proteins of unknown architecture, the mutation maps showed several positions where disulfide bridging might occur.

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The protein data bank: A computer-based archival file for macromolecular structures

Cited by 1,128 publications

References 8 publications

Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage

Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage

Acetylcholinesterase Inhibitors with Photoswitchable Inhibition of β-Amyloid Aggregation

Paired natural cysteine mutation mapping: Aid to constraining models of protein tertiary structure

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