Untitled

Mahato, Sourav; De, Debojyoti; Dutta, Debajyoti; Kundu, Moloy; Bhattacharya, Subhamoy; Schiavone, Marc; Bhattacharya, Sanjoy K.

doi:10.1186/1475-2859-3-7

Cited by 3 publications

(3 citation statements)

References 134 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Finally, the information contained in the MD simulations will be used to address some unresolved issues in the experimental PEPCK literature, including the role of an active site lid in achieving optimal enzymatic efficiency . Overall, the results of this work will offer guidance to future efforts designing bioinspired CO 2 capture and sequestration systems …”

Section: Introductionmentioning

confidence: 98%

See 1 more Smart Citation

Nature of Protein–CO₂ Interactions as Elucidated via Molecular Dynamics

2012

View full text Add to dashboard Cite

Rising global temperatures require innovative measures to reduce atmospheric concentrations of CO(2). The most successful carbon capture technology on Earth is the enzymatic capture of CO(2) and its sequestration in the form of glucose. Efforts to improve upon or mimic this naturally occurring process will require a rich understanding of protein-CO(2) interactions. Toward that end, extensive all-atom molecular dynamics (MD) simulations were performed on the CO(2)-utilizing enzyme phosphoenolpyruvate carboxykinase (PEPCK). Preliminary simulations were performed using implicit and explicit solvent models, which yielded similar results: arginine, lysine, tyrosine, and asparagine enhance the ability of a protein to bind carbon dioxide. Extensive explicit solvent simulations were performed for both wild-type PEPCK and five single-point PEPCK mutants, revealing three prevalent channels by which CO(2) enters (or exits) the active site cleft, as well as a fourth channel (observed only once), the existence of which can be rationalized in terms of the position of a key Arg residue. The strongest CO(2) binding sites in these simulations consist of appropriately positioned hydrogen bond donors and acceptors. Interactions between CO(2) and both Mn(2+) and Mg(2+) present in PEPCK are minimal due to the stable protein- and solvent-based coordination environments of these cations. His 232, suggested by X-ray crystallography as being a potential important CO(2) binding site, is indeed found to be particularly "CO(2)-philic" in these simulations. Finally, a recent mechanism, proposed on the basis of X-ray crystallography, for PEPCK active site lid closure is discussed in light of the MD trajectories. Overall, the results of this work will prove useful not only to scientists investigating PEPCK, but also to groups seeking to develop an environmentally benign, protein-based carbon capture, sequestration, and utilization system.

show abstract

Section: Introductionmentioning

confidence: 98%

“…26 Overall, the results of this work will offer guidance to future efforts designing bioinspired CO 2 capture and sequestration systems. 38 2. COMPUTATIONAL METHODS 2.1.…”

Section: Introductionmentioning

confidence: 99%

Nature of Protein–CO₂ Interactions as Elucidated via Molecular Dynamics

2012

View full text Add to dashboard Cite

show abstract

“…For example, N 2 is fixed by bacterial nitrogenases, O 2 and CO 2 are transported in the blood by hemoglobin, NO controls vasodilation, and CO 2 is fixed in the Calvin cycle by the enzyme RuBisCO . This last, the enzymatic utilization of carbon dioxide, not only represents the ultimate energy source for all higher life, but has also recently been scrutinized in the context of developing biotechnological approaches − to ameliorate rising levels of atmospheric CO 2 . Recent research detailing protein–CO 2 interactions has revealed patterns in primary, secondary, and tertiary protein structure that influence carbon dioxide binding affinity.…”

mentioning

confidence: 99%

Carbon Dioxide Migration Pathways in Proteins

Drummond

Wilson

Cundari

2012

J. Phys. Chem. Lett.

View full text Add to dashboard Cite

Some of the most important biological processes, such as carbon fixation, are dependent on protein-gas interactions. The motion of CO2 through the enzyme phosphoenolpyruvate carboxykinase was investigated using extensive all-atom molecular dynamics simulations. Three discrete migration pathways were located, suggesting the protein directs the movement of CO2. The chemical nature of these pathways is discussed, as are their biotechnological ramifications.

show abstract

Untitled

Dutta

Kundu

et al. 2005

Microb Cell Fact

Self Cite

View full text Add to dashboard Cite

Background: Carbon dioxide fixation bioprocess in reactors necessitates recycling of D-ribulose1,5-bisphosphate (RuBP) for continuous operation. A radically new close loop of RuBP regenerating reactor design has been proposed that will harbor enzyme-complexes instead of purified enzymes. These reactors will need binders enabling selective capture and release of sugar and intermediate metabolites enabling specific conversions during regeneration. In the current manuscript we describe properties of proteins that will act as potential binders in RuBP regeneration reactors.

show abstract

Untitled

Abstract: Sugar binding proteins and binders of intermediate sugar metabolites derived from microbes are increasingly being used as reagents in new and expanding areas of biotechnology.

Cited by 3 publications

References 134 publications

Nature of Protein–CO₂ Interactions as Elucidated via Molecular Dynamics

Nature of Protein–CO₂ Interactions as Elucidated via Molecular Dynamics

Carbon Dioxide Migration Pathways in Proteins

Untitled

Contact Info

Product

Resources

About

Untitled

Abstract: Sugar binding proteins and binders of intermediate sugar metabolites derived from microbes are increasingly being used as reagents in new and expanding areas of biotechnology.

Cited by 3 publications

References 134 publications

Nature of Protein–CO2 Interactions as Elucidated via Molecular Dynamics

Nature of Protein–CO2 Interactions as Elucidated via Molecular Dynamics

Carbon Dioxide Migration Pathways in Proteins

Untitled

Contact Info

Product

Resources

About

Nature of Protein–CO₂ Interactions as Elucidated via Molecular Dynamics

Nature of Protein–CO₂ Interactions as Elucidated via Molecular Dynamics