Structure of the coat protein-binding domain of the scaffolding protein from a double-stranded DNA virus11Edited by M. Summers

Sun, Yahong; Parker, Matthew H.; Weigele, Peter; Casjens, Sherwood; Prevelige, Peter E.; Krishna, N. Rama

doi:10.1006/jmbi.2000.3620

Cited by 76 publications

(105 citation statements)

References 36 publications

(36 reference statements)

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“…5a). The NMR structure of this fragment shows amino acids 269 -303 folded into the HTH domain and amino acids 238 -268 as random coil (50). In addition, the T265W substitution does not have a significant effect on the secondary structure.…”

Section: Design Of Mutations That Affect the Zipper Core And Turn Of mentioning

confidence: 89%

“…1) (50). The turn/loop residues are Ala-284 to Ala-288 (50). Even though residues Asn-272 and Ile-302 are not part of the hydrophobic zipper, they are adjacent to the N-terminal end of helix 1 and C-terminal end of helix 2, respec- (50) was modeled using PyMOL (PyMOL Molecular Graphics System, version 1.3r1, Schrödinger, LLC).…”

Section: Design Of Mutations That Affect the Zipper Core And Turn Of mentioning

confidence: 99%

“…The turn is stabilized by i, iϩ3 hydrogen bond interaction of the main chain CO group of Ala-284 and main chain NH group of Gly-287, thereby classifying it as a type 1 ␤-turn (50,65). Residues Val-289, Glu-290, and Thr-291 are at the N terminus of helix 2, and are not part of the hydrophobic core of the zipper.…”

Section: Design Of Mutations That Affect the Zipper Core And Turn Of mentioning

confidence: 99%

“…(ii) Val-289 could make a specific hydrophobic contact with coat protein that is required for this interaction (50). The V289D variant can weakly nucleate assembly of coat proteins and binding to procapsid shells is completely abolished.…”

Section: The Structure Of the Scaffolding Protein C-terminal Hth Ismentioning

confidence: 99%

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Unraveling the Role of the C-terminal Helix Turn Helix of the Coat-binding Domain of Bacteriophage P22 Scaffolding Protein

Padilla-Meier

Gilcrease

Weigele

et al. 2012

Journal of Biological Chemistry

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Background: Viral scaffolding proteins interact with coat proteins to drive procapsid assembly. Results: Amino acid substitutions in the turn and between the helices of the coat protein-binding domain of scaffolding protein block procapsid assembly. Conclusion:The orientation of helices in the scaffolding helix turn helix domain is critical for procapsid assembly. Significance: Understanding scaffolding/coat protein interactions illuminates the mechanism of assembly of many large viruses.

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Section: Design Of Mutations That Affect the Zipper Core And Turn Of mentioning

confidence: 89%

Section: Design Of Mutations That Affect the Zipper Core And Turn Of mentioning

confidence: 99%

Section: Design Of Mutations That Affect the Zipper Core And Turn Of mentioning

confidence: 99%

Section: The Structure Of the Scaffolding Protein C-terminal Hth Ismentioning

confidence: 99%

See 2 more Smart Citations

Unraveling the Role of the C-terminal Helix Turn Helix of the Coat-binding Domain of Bacteriophage P22 Scaffolding Protein

Padilla-Meier

Gilcrease

Weigele

et al. 2012

Journal of Biological Chemistry

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“…These processes were first studied with phages T4 and lambda using optical diffraction of negatively stained micrographs [6,13]. Subsequently, these processes have been studied at higher resolution by cryo-electron microscopy [1,7,9,10,12]. For phage P22, the hexagonal array of subunits at local six-fold axes are distinctively skewed, with a hole in the centre.…”

Section: Introductionmentioning

confidence: 99%

Lattice Transformations and Subunit Conformational Changes in Phage Capsid Maturation

Gossard

King

2005

Computational and Mathematical Methods in Medicine

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A general feature of the pathways for the assembly of double-stranded DNA phages and viruses is the assembly of coat and scaffolding subunits into a precursor shell or procapsid, followed by packaging of the genomic DNA into the shell. Coupled to this DNA packaging process is the loss of the scaffolding subunits and expansion and re-organization of the procapsid lattice to the lattice of the mature virus. Such lattice transitions have also been observed with adenoviruses and herpesviruses. In re-organizing into the mature capsid lattice, each subunit of the precursor lattice must change its conformation, or its relationship with its neighbours, or both. We briefly review here recent structural data for phages P22 and HK97, and describe the motions and conformational changes associated with this lattice transition. Possible functions of such constrained transformations within the virus life-cycle are discussed.

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Geometry and vibrational frequencies of the helical polypeptide complexes with ligand molecules

Makshakova

Чачков

Ермакова

2011

Int J of Quantum Chemistry

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The complexes of alpha helical polypeptides and individual molecules of water, acetonitrile, and 1,4-dioxane have been investigated. We used 16-mer of polyalanine (PA), polyglutamic acid (PGA) and poly-c-benzyl-L-glutamate (PBG). Full geometry optimization was performed for polypeptides and their complexes with ligands, each structure has been characterized by the vibrational analysis and the interaction energy including the correction for zero point vibrational energy. Polyalanine creates by single complex with water molecule, acetonitrile, and dioxane. Polyglutamic acid forms five different complexes with water molecule, and three complexes with acetonitrile and two complexes with dioxane. Two complexes of poly-c-benzyl-L-glutamate with each ligand were found. Carbonyl oxygen of PGA and PBG confirms its strong acceptor character by participation in formation of all obtained complexes with water and acetonitrile. The long side chains of PGA and PBG aid the formation of complexes with two hydrogen bonds where ligand molecule bridges two polar sites of polypeptide. Most of complexes of dioxane with polypeptides are produced due to weak hydrogen bonds of type CAHÁÁÁO. Strong shifts for the stretching vibrations of the interacting group of polypeptides and ligands under the complex formation are detected. Obtained frequencies are in a good agreement with known experimental data.

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Structure of the coat protein-binding domain of the scaffolding protein from a double-stranded DNA virus11Edited by M. Summers

Cited by 76 publications

References 36 publications

Unraveling the Role of the C-terminal Helix Turn Helix of the Coat-binding Domain of Bacteriophage P22 Scaffolding Protein

Unraveling the Role of the C-terminal Helix Turn Helix of the Coat-binding Domain of Bacteriophage P22 Scaffolding Protein

Lattice Transformations and Subunit Conformational Changes in Phage Capsid Maturation

Geometry and vibrational frequencies of the helical polypeptide complexes with ligand molecules

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