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Comparative studies for evaluation of CO₂ fixation in the cavity of the Rubisco enzyme using QM, QM/MM and linear-scaling DFT methods.

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We evaluate the minimum energy configuration (MM) and binding free energy (QM/MM and QM) of CO2 to Rubisco, of fundamental importance to the carboxylation step of the reaction. Two structural motifs have been used to achieve this goal, one of which starts from the initial X-ray Protein Data Bank

Diffusion and interactions of carbon dioxide and oxygen in the vicinity of the active site of Rubisco: molecular dynamics and quantum chemical studies.

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Molecular dynamics (MD) at the molecular mechanical level and geometry optimisation at the quantum mechanical level have been performed to investigate the transport and fixation of oxygen and carbon dioxide in the cavity of ribulose-1,5-bisphosphate carboxylase/oxygenase, or Rubisco. Multiple MD

Putative functional role for the invariant aspartate 263 residue of Rhodospirillum rubrum Rubisco.

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Although aspartate residue D263 of Rhodospirillum rubrum Rubisco is close to the active site and invariant in all reported Rubiscos, its possible functional and structural roles in Rubisco activity have not been investigated. We have mutagenised D263 to several selected amino acids (asparagine,

Perturbed ATPase activity and not "close confinement" of substrate in the cis cavity affects rates of folding by tail-multiplied GroEL.

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Folding of substrate proteins inside the sequestered and hydrophilic GroEL-GroES cis cavity favors production of the native state. Recent studies of GroEL molecules containing volume-occupying multiplications of the flexible C-terminal tail segments have been interpreted to indicate that close

CO2 and O2 distribution in Rubisco suggests the small subunit functions as a CO2 reservoir.

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Protein-gas interactions are important in biology. The enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes two competing reactions involving CO2 and O2 as substrates. Carboxylation of the common substrate ribulose-1,5-bisphosphate leads to photosynthetic carbon assimilation,

Midday depression of net photosynthesis in the tropical rainforest tree Eperua grandiflora: contributions of stomatal and internal conductances, respiration and Rubisco functioning.

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High midday temperatures can depress net photosynthesis. We investigated possible mechanisms underlying this phenomenon in leaves of Eperua grandiflora (Aubl.) Benth. saplings. This tropical tree establishes in small gaps in the rainforest canopy where direct sunlight can raise midday temperatures

Variable mesophyll conductance revisited: theoretical background and experimental implications.

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The CO(2) concentration at the site of carboxylation inside the chloroplast stroma depends not only on the stomatal conductance, but also on the conductance of CO(2) between substomatal cavities and the site of CO(2) fixation. This conductance, commonly termed mesophyll conductance (g(m) ),

Tandem mass spectrometry of intact GroEL-substrate complexes reveals substrate-specific conformational changes in the trans ring.

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It has been suggested that the bacterial GroEL chaperonin accommodates only one substrate at any given time, due to conformational changes to both the cis and trans ring that are induced upon substrate binding. Using electrospray ionization mass spectrometry, we show that indeed GroEL binds only one

Presence of Hydrogenophilus thermoluteolus DNA in accretion ice in the subglacial Lake Vostok, Antarctica, assessed using rrs, cbb and hox.

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The 3561 m Vostok ice core sample originating from the subglacial Lake Vostok accretion (frozen lake water) ice with sediment inclusions was thoroughly studied by various means to confirm the presence of the thermophile bacterium Hydrogenophilus thermoluteolus reported earlier in the 3607 m

The kinetics of conformation change as determinant of Rubisco's specificity.

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The molecular basis of Rubisco's specificity is investigated in terms of the structure and kinetics of the enzyme. We propose that the rates of the conformational changes (closing/opening) of the binding niche exert a crucial influence on apparent binding rates and the enzyme's specificity. An

Structural insight into the cooperation of chloroplast chaperonin subunits.

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BACKGROUND Chloroplast chaperonin, consisting of multiple subunits, mediates folding of the highly abundant protein Rubisco with the assistance of co-chaperonins. ATP hydrolysis drives the chaperonin allosteric cycle to assist substrate folding and promotes disassembly of chloroplast chaperonin. The

Leaf photosynthesis and respiration of three bioenergy crops in relation to temperature and leaf nitrogen: how conserved are biochemical model parameters among crop species?

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Given the need for parallel increases in food and energy production from crops in the context of global change, crop simulation models and data sets to feed these models with photosynthesis and respiration parameters are increasingly important. This study provides information on photosynthesis and

The photosynthetic limitation posed by internal conductance to CO2 movement is increased by nutrient supply.

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The internal conductance to CO(2) supply from substomatal cavities to sites of carboxylation may pose a large limitation to photosynthesis, but little is known of how it is affected by nutrient supply. Knowing how internal conductance responds to nutrient supply is critical for interpreting the

Multivalent binding of nonnative substrate proteins by the chaperonin GroEL.

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The chaperonin GroEL binds nonnative substrate protein in the central cavity of an open ring through exposed hydrophobic residues at the inside aspect of the apical domains and then mediates productive folding upon binding ATP and the cochaperonin GroES. Whether nonnative proteins bind to more than

Characterization of a functional GroEL14(GroES7)2 chaperonin hetero-oligomer.

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Chaperonins GroEL and GroES form two types of hetero-oligomers in vitro that can mediate the folding of proteins. Chemical cross-linking and electron microscopy showed that in the presence of adenosine triphosphate (ATP), two GroES7 rings can successively bind a single GroEL14 core oligomer. The

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