Fibrinogen: A preliminary analysis of the amino acid sequences of the portions of the α, β and γ-chains postulated to form the interdomainal link between globular regions of the molecule

Parry, D.A.D.

doi:10.1016/0022-2836(78)90353-4

Cited by 30 publications

(9 citation statements)

References 10 publications

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“…'Skips' are insertions of one residue into the heptad pattern [7], 'stammers' result through an insertion of three additional residues [8][9][10], and 'stutters' appear if four additional residues interrupt the heptad sequence [11]. Presence of a stutter results in an almost parallel run of both AHs without interrupting the CC geometry.…”

Section: The Molecular Architecture Of Vimentin Intermediate Filamentsmentioning

confidence: 98%

Molecular Mechanics of Stutter Defects in Vimentin Intermediate Filaments

Ackbarow

Buehler

2007

Exp Mech

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Vimentin coiled-coil alpha-helical dimers are elementary protein building blocks of intermediate filaments, an important component of the cell's cytoskeleton.All intermediate filament dimers feature a highly conserved 'stutter' region, a sequence of amino acids that interrupts the superhelical coiled-coil arrangement of the two alphahelices, leading to a parallel arrangement of the alphahelices in this region. Earlier studies have suggested that the stutter plays an important role in filament assembly. Here we show that the stutter also has a significant effect on the mechanical behavior of vimentin dimers. We develop an Extended Bell Model to provide a theoretical description of the unfolding behavior of coiled-coil structures, capable of capturing different molecular geometries and loading rates. The Extended Bell Model predicts that the stutter represents a molecular defect at which unfolding occurs at lower forces than in the rest of the protein. Our studies suggest that the presence of the stutter leads to a softer structure with more homogeneous plastic strain distribution under deformation. The predictions by the Extended Bell Model are confirmed by large-scale MD simulations of three model systems: Two parallel alpha-helices, a coiled-coil dimer, as well as a coiled-coil dimer with a stutter. The simulations prove that in agreement with the prediction based on our Extended Bell Model, the stutter represents the locations at which the protein structure has the least resistance to unfolding. We discuss the implications of this molecular architecture in terms of its biological function.

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Section: The Molecular Architecture Of Vimentin Intermediate Filamentsmentioning

confidence: 98%

Molecular Mechanics of Stutter Defects in Vimentin Intermediate Filaments

Ackbarow

Buehler

2007

Exp Mech

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“…Judging by electron microscopy studies these domains are attached by rod-like connectors [2,3] which were supposed to have a coiled-coil structure [4]. The regions with a specific sequence for coiled-coils were indeed revealed in the fibrinogen polypeptide chains between the two 'disulfide rings' at each half of the molecule [5,6]. Our denaturation studies showed that the D fragment of fibrinogen, corresponding to both its terminal parts, consists of 2 structures with a drastically different stability [7].…”

Section: Introductionmentioning

confidence: 99%

Isolation of thermostable structure from the fibrinogen D Fragment

1982

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“…At the molecular level of coiled coils, patterns of heptad repeats have been observed that contain hydrophobic amino acids alternately located three and four residues apart [1]. The positions of these repeats are usually labeled alphabetically (a -g) with registers of "a" and "d" that represent the positions of hydrophobic residues.…”

Section: Introductionmentioning

confidence: 99%

“…Regular heptad repeat patterns are sometimes broken by nonheptad inserts [2][3][4], generally described as heptad breaks. Four types of heptad breaks have been reported [4,5]: (1) The stutter is the break in which three residues are deleted from the heptad repeats [1]. It has the tendency to loosen the supercoiling locally.…”

Section: Introductionmentioning

confidence: 99%

Prediction of fragile points of coiled coils

Tanizawa

Taniguchi²,

Ghimire³

et al. 2009

CBIJ

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A prediction system for identifying the region of flexible regions of the coiled coil was developed to determine the bending positions of the myosin rods using atomic force microscopy (AFM) and to analyze the molecular structures of proteins containing coiled coils. The prediction system comprises two modules: identification of heptad break points and prediction of fragile points in the coiled coil due to the hydrophilic core or hydrophobic outfield region. Here, we investigated the myosin rods using this prediction system. The results of AFM imaging showed four main flexible regions in a single myosin rod and of the 17 possible fragile points predicted, 16 were located in the four experimental bending regions. Next, we examined the enhanced fluctuation around these predicted fragile points using the B-factor for the three dimensional structure of coiled coil proteins from the SCOP database and found that the fluctuations in the hydrophilic core regions were significantly larger than those in the regions of the normal coiled coil. In contrast, the fluctuations in the hydrophobic outfield regions were reduced, suggesting a structural change of the coiled coils to balance these regions. Thus, the dynamic changes in the structure of the coiled coils around the fragile points may be related to the biological functions of the proteins. The prediction tool which developed in this work was incorporated in the SOSUIcoil system which predicts the coiled coil regions.

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Fibrinogen: A preliminary analysis of the amino acid sequences of the portions of the α, β and γ-chains postulated to form the interdomainal link between globular regions of the molecule

Cited by 30 publications

References 10 publications

Molecular Mechanics of Stutter Defects in Vimentin Intermediate Filaments

Molecular Mechanics of Stutter Defects in Vimentin Intermediate Filaments

Isolation of thermostable structure from the fibrinogen D Fragment

Prediction of fragile points of coiled coils

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