Metal-Coupled Folding of Cys<sub>2</sub>His<sub>2</sub> Zinc-Finger

Li, Wenfei; Jian, Zhang; Wang, Jun; Wang, Wei

doi:10.1021/ja075302g

Cited by 116 publications

(133 citation statements)

References 74 publications

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“…Similarly, in BABZ7 and BABZ8, the mutations essentially destroyed the hydrophobic core. So the overall folding involves a delicate interplay of hydrophobic packing, hydrogen bonding, and metal binding (Li et al, 2007(Li et al, , 2008. In addition, if the coordination residues are located on flexible terminals or loops, as in BABZ2 and BABZ4, zinc binding-induced aggregation may occur, especially for the small protein like βαβ, so the entropy cost to fix the coordination residues at specific conformations should be considered, as zinc binding in proteins is an entropy-driven process (Reddi et al, 2007).…”

Section: Discussionmentioning

confidence: 99%

Engineering a zinc binding site into the de novo designed protein DS119 with a βαβ structure

Zhu¹,

Liang²,

Lai³

2011

Protein Cell

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Functional proteins designed de novo have potential application in chemical engineering, agriculture and healthcare. Metal binding sites are commonly used to incorporate functions. Based on a de novo designed protein DS119 with a βαβ structure, we have computationally engineered zinc binding sites into it using a home-made searching program. Seven out of the eight designed sequences tested were shown to bind Zn 2+ with micromolar affinity, and one of them bound Zn 2+ with 1:1 stoichiometry. This is the first time that metalloproteins with an α, β mixed structure have been designed from scratch.

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Section: Discussionmentioning

confidence: 99%

Engineering a zinc binding site into the de novo designed protein DS119 with a βαβ structure

Zhu¹,

Liang²,

Lai³

2011

Protein Cell

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“…The metal ion induced protonation/deprotonation of ligand residues and the metal-induced polarization effect of the imidazole ring in the histidine residues were implemented by an empirical way (See ref. (165) for the the details). With these modifications, the metal coupled protein folding and other functional motions can be appropriately described by classical MD method.…”

Section: Metal-coupled Protein Foldingmentioning

confidence: 99%

“…These results again suggested that the Zn(II) is actively involved in the whole folding process, and its binding can direct and modulate the folding and stabilization of the secondary structures. Also, this crucial role of zinc binding is mediated by the packing of the conserved hydrophobic residues (165).…”

Section: Metal-coupled Protein Foldingmentioning

confidence: 99%

Protein folding simulations: From coarse‐grained model to all‐atom model

Jian

Wang

et al. 2009

IUBMB Life

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SummaryProtein folding is an important and challenging problem in molecular biology. During the last two decades, molecular dynamics (MD) simulation has proved to be a paramount tool and was widely used to study protein structures, folding kinetics and thermodynamics, and structure-stability-function relationship. It was also used to help engineering and designing new proteins, and to answer even more general questions such as the minimal number of amino acid or the evolution principle of protein families. Nowadays, the MD simulation is still undergoing rapid developments. The first trend is to toward developing new coarse-grained models and studying larger and more complex molecular systems such as protein-protein complex and their assembling process, amyloid related aggregations, and structure and motion of chaperons, motors, channels and virus capsides; the second trend is toward building high resolution models and explore more detailed and accurate pictures of protein folding and the associated processes, such as the coordination bond or disulfide bond involved folding, the polarization, charge transfer and protonate/deprotonate process involved in metal coupled folding, and the ion permeation and its coupling with the kinetics of channels. On these new territories, MD simulations have given many promising results and will continue to offer exciting views. Here, we review several new subjects investigated by using MD simulations as well as the corresponding developments of appropriate protein models. These include but are not limited to the attempt to go beyond the topology based Gō-like model and characterize the energetic factors in protein structures and dynamics, the study of the thermodynamics and kinetics of disulfide bond involved protein folding, the modeling of the interactions between chaperonin and the encapsulated protein and the protein folding under this circumstance, the effort to clarify the important yet still elusive folding mechanism of protein BBL, the development of discrete MD and its application in studying the a-b conformational conversion and oligomer assembling process, and the modeling of metal ion involved protein folding.

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“…The computational simulations, on the other hand, might mimic and model this kind of interactions and avoid some complicated side effects. Molecular dynamics (MD) is one of these computational techniques, which is widely used in the studies of biomolecules [38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54][55], and nanoscale systems [56][57][58][59][60]. It is found effective in providing insights to the interactions between proteins and CNTs.…”

Section: Introductionmentioning

confidence: 99%