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- Van Lun, Michiel, et al.
(författare)
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CO2 and O-2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir
- 2014
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 136:8, s. 3165-3171
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Tidskriftsartikel (refereegranskat)abstract
- Protein gas interactions are important in biology. The enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes two competing reactions involving CO2 and O-2 as substrates. Carboxylation of the common substrate ribulose-1,5-bisphosphate leads to photosynthetic carbon assimilation, while the oxygenation reaction competes with carboxylation and reduces photosynthetic productivity. The migration of the two gases in and around Rubisco was investigated using molecular dynamics simulations. The results indicate that at equal concentrations of the gases, Rubisco binds CO2 stronger than it does O-2. Amino acids with small hydrophobic side chains are the most proficient in attracting CO2, indicating a significant contribution of the hydrophobic effect in the interaction. On average, residues in the small subunit bind approximately twice as much CO2 as do residues in the large subunit. We did not detect any cavities that would provide a route to the active site for the gases. Instead, CO2 appears to be guided toward the active site through a CO2 binding region around the active site opening that extends to the closest neighboring small subunits. Taken together, these results suggest the small subunit may function as a "reservoir" for CO2 storage.
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| 3. |
- Van Lun, Michiel, et al.
(författare)
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Subunit Interface Dynamics in Hexadecameric Rubisco
- 2011
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 411:5, s. 1083-1098
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Tidskriftsartikel (refereegranskat)abstract
- Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) plays an important role in the global carbon cycle as a hub for biomass. Rubisco catalyzes not only the carboxylation of RuBP with carbon dioxide but also a competing oxygenation reaction of RuBP with a negative impact on photosynthetic yield. The functional active site is built from two large (L) subunits that form a dimer. The octameric core of four L(2) dimers is held at each end by a cluster of four small (S) subunits, forming a hexadecamer. Each large subunit contacts more than one S subunit. These interactions exploit the dynamic flexibility of Rubisco, which we address in this study. Here, we describe seven different types of interfaces of hexadecameric Rubisco. We have analyzed these interfaces with respect to the size of the interface area and the number of polar interactions, including salt bridges and hydrogen bonds in a variety of Rubisco enzymes from different organisms and different kingdoms of life, including the Rubisco-like proteins. We have also performed molecular dynamics simulations of Rubisco from Chlamydomonas reinhardtii and mutants thereof. From our computational analyses, we propose structural checkpoints of the S subunit to ensure the functionality and/or assembly of the Rubisco holoenzyme. These checkpoints appear to fine-tune the dynamics of the enzyme in a way that could influence enzyme performance.
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- Yim, Chi Ming, et al.
(författare)
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CO and O overlayers on Pd nanocrystals supported on TiO2(110)
- 2013
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Ingår i: Faraday Discussions. - : Royal Society of Chemistry (RSC). - 1364-5498 .- 1359-6640. ; 162, s. 191-200
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Tidskriftsartikel (refereegranskat)abstract
- We have prepared a model catalytic system by depositing Pd onto a TiO2(110) surface held at similar to 720 K. Scanning tunneling microscopy (STM) reveals well-defined Pd nanocrystals consisting of (111) top facets with {111} and {100} side facets. The Pd nanocrystals go down to about 10 nm in width and 1.3 nm in height. Top facets can be imaged with atomic resolution, indicating the absence of TiOx encapsulation. The model catalyst was probed by exposure to CO and O-2. By varying the CO exposure, different CO overlayers were formed on the (111) top facets, with coverages ranging from 0.33 to 0.75 of a monolayer. Near edge X-ray absorption fine structure (NEXAFS) measurements at 300 K reveal that at around 0.5 ML coverage, CO is oriented with the molecular axis more or less normal to TiO2(110). Dosing small amounts of O-2 separately on a Pd/TiO2(110) surface led to an overlayer of p(2 x 2)-O formed on the (111) top facet of the Pd nanocrystals at 190 K.
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