Abstract：
:Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and structural refinement of macrobiomolecules (e.g., proteins and nucleic acids). These methods are highly efficient, since they implement quantum chemistry techniques for modeling only the small part of the system (QM layer) that undergoes chemical modifications, charge transfer, etc., under the influence of the surrounding environment. The rest of the system (MM layer) is described in terms of molecular mechanics force fields, assuming that its influence on the QM layer can be roughly decomposed in terms of electrostatic interactions and steric hindrance. Common limitations of QM/MM methods include inaccuracies in the MM force fields, when polarization effects are not explicitly considered, and the approximate treatment of electrostatic interactions at the boundaries between QM and MM layers. This article reviews recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in extended systems beyond the common limitations of QM/MM hybrid methods. We focus on the moving-domain QM/MM (MoD-QM/MM) methodology that partitions the system into many molecular domains and obtains the electrostatic and structural properties of the whole system from an iterative self-consistent treatment of the constituent molecular fragments. We illustrate the MoD-QM/MM method as applied to the description of photosystem II as well as in conjunction with the application of spectroscopically constrained QM/MM optimization methods, based on high-resolution spectroscopic data (extended X-ray absorption fine structure spectra, and exchange coupling constants).
journal_name
Photosynth Resjournal_title
Photosynthesis researchauthors
Sproviero EM,Newcomer MB,Gascón JA,Batista ER,Brudvig GW,Batista VSdoi
10.1007/s11120-009-9467-6subject
Has Abstractpub_date
2009-11-01 00:00:00pages
455-70issue
2-3eissn
0166-8595issn
1573-5079journal_volume
102pub_type
杂志文章,评审abstract：:Biohybrid light-harvesting architectures can be constructed that employ native-like bacterial photosynthetic antenna peptides as a scaffold to which synthetic chromophores are attached to augment overall spectral coverage. Synthetic bacteriochlorins are attractive to enhance capture of solar radiation in the photon-ri...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/s11120-014-0021-9
更新日期：2014-11-01 00:00:00
abstract：:Modulation of the efficiency with which leaves convert absorbed light to photochemical energy [intrinsic efficiency of open photosystem II (PSII) centers, as the ratio of variable to maximal chlorophyll fluorescence] as well as leaf xanthophyll composition (interconversions of the xanthophyll cycle pigments violaxanth...
journal_title：Photosynthesis research
pub_type： 杂志文章,评审
doi：10.1007/s11120-012-9761-6
更新日期：2012-09-01 00:00:00
abstract：:The excitation energy transfer between carotenoid and chlorophyll (Chl) in the cytochrome b ( 6 ) f complex from Bryopsis corticulans (B. corticulans), in which the carotenoid is 9-cis-alpha-carotene, was investigated by means of fluorescence excitation and sub-microsecond time-resolved absorption spectroscopies. The ...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/s11120-005-9020-1
更新日期：2006-04-01 00:00:00
abstract：:Illumination of the dark-incubated cells of Synechocystis PCC6803 caused recovery of both respiratory activity of oxygen uptake and PS I-cyclic electron flow, which was monitored by the dark reduction of P700(+) in the presence of DCMU after a 50 ms pulse light (MT) under background far-red light, but the effects were...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1023/A:1017946524199
更新日期：2001-01-01 00:00:00
abstract：:The content and composition of pigments and acyl lipids (monogalactosyl diacylglycerol, digalactosyl diacylglycerol and phosphatidyl glycerol) have been investigated in developing chloroplasts isolated from successive 2-cm sections along the leaves of wheat seedlings grown either under 100, 30 or 3 W·m(-2). In all exa...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/BF00035244
更新日期：1986-01-01 00:00:00
abstract：:Light energy harvested by the pigments in Photosystem I (PSI) is used for charge separation in the reaction center (RC), after which the positive charge resides on a special chlorophyll dimer called P700. In studies on the PSI trapping kinetics, P700(+) is usually chemically reduced to re-open the RCs. So far, the inf...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/s11120-011-9671-z
更新日期：2012-03-01 00:00:00
abstract：:Bioenergetic properties of thylakoids from plants submitted to a water stress stress (watering stopped for 6-15 days) have been measured in two lupin genotypes characterized as resistant or susceptible to drought. This energy coupling was assessed by flow-force relationships relating the phosphorylation rate to the ma...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/BF00035944
更新日期：1992-05-01 00:00:00
abstract：:Oxygenic photosynthesis is driven by two multi-subunit membrane protein complexes, Photosystem I and Photosystem II. In plants and green algae, both complexes are composed of two moieties: a reaction center (RC), where light-induced charge translocation occurs, and a peripheral antenna that absorbs light and funnels i...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1023/B:PRES.0000036881.23512.42
更新日期：2004-01-01 00:00:00
abstract：:Photosynthesis powers our planet and is a source of inspiration for developing artificial constructs mimicking many aspects of the natural energy transducing process. In the complex machinery of photosystem II (PSII), the redox activity of the tyrosine Z (Tyrz) hydrogen-bonded to histidine 190 (His190) is essential fo...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/s11120-020-00815-x
更新日期：2021-01-11 00:00:00
abstract：:The author gives an autobiographical sketch of his path to chlorophyll research, and describes some results. The discussion is largely focused on long wavelength forms of chlorophyll and how they might be generated by self-assembly. Dimers or oligomers, (Chl)n, result from coordination interactions between the central...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/BF00033128
更新日期：1990-12-01 00:00:00
abstract：:The filamentous nitrogen-fixing cyanobacterium, Anabaena sp. strain PCC 7120 was found to tolerate very high doses of 60Co-gamma radiation or prolonged desiccation. Post-stress, cells remained intact and revived all the vital functions. A remarkable capacity to repair highly disintegrated genome and recycle the damage...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/s11120-013-9936-9
更新日期：2013-10-12 00:00:00
abstract：:A peptide ranging from residue 229 to 240 of the D1 protein of Photosystem (PS) II was synthesized and lanthanides were used as candidates of calcium. Fluorescence and FTIR spectroscopy were used to test the conformational adaptation after lanthanide additions. Fluorescence spectroscopy showed that the synthetic pepti...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/BF00048603
更新日期：1995-06-01 00:00:00
abstract：:Previous investigations have shown that increased source strength as a result of elevated CO(2) can alter the timing of the phases of change that occur in photosynthetic rates during dicot leaf ontogeny [Miller et al. (1997) Plant Physiol 115: 1195-1200]. To evaluate the converse situation of decreased source strength...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1023/A:1006367719639
更新日期：2000-01-01 00:00:00
abstract：:Although it has been believed that wild-type plants are capable of protecting photosystem I (PSI) under high light, our previous study indicates that PSI is sensitive to high light in the shade-established tree species Psychotria rubra. However, the underlying physiological mechanisms are unclear. In this study, we ex...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/s11120-016-0275-5
更新日期：2016-07-01 00:00:00
abstract：:The polypeptide composition of thylakoid membranes of the red alga Cyanidium caldarium was studied by PAGE in the presence of lithium dodecyl sulfate. The thylakoid membranes were shown to contain 65 polypeptides with mol wt from 110 to 10 kDa. PS I isolated from C. caldarium cells is composed of at least 5 components...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/BF00035678
更新日期：1991-10-01 00:00:00
abstract：:Chlorophyll f is a photosynthetic pigment that was discovered in 2010. In this study, we present investigations on spectral and dynamic characteristics of singlet-excited and triplet states of Chl f with the application of ultrafast time-resolved absorption and fluorescence spectroscopies. The pigment was studied at r...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/s11120-014-9981-z
更新日期：2014-07-01 00:00:00
abstract：:Cyanobacteria, algae, and plants produce dioxygen from water. Driven and clocked by light quanta, the catalytic Mn(4)Ca Tyrosine centre accumulates four oxidizing equivalents before it abstracts four electrons from water and liberates dioxygen and protons. Intermediates of this reaction cascade are short-lived (<100 m...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/s11120-008-9321-2
更新日期：2008-10-01 00:00:00
abstract：:We investigated the dark-to-light transition in Synechococcus sp. PCC 7942 cells by a detailed analysis of fluorescence transients induced by strong red light. The transients, recorded with high data-acquisition, revealed all the steps of the fast (OJIP; 10(-5)-1 s) and slow phase (PSM(T); 1-10(3) s), kinetically dist...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/s11120-009-9405-7
更新日期：2009-03-01 00:00:00
abstract：:Photosynthesis was well-established on the earth at least 3.5 thousand million years ago, and it is widely believed that these ancient organisms had similar metabolic capabilities to modern cyanobacteria. This requires that development of two photosystems and the oxygen evolution capability occurred very early in the...
journal_title：Photosynthesis research
pub_type： 杂志文章,评审
doi：
更新日期：1992-01-01 00:00:00
abstract：:The potential role of foliar carbon export features in the acclimation of photosynthetic capacity to differences and changes in light environment was evaluated. These features included apoplastic vs. symplastic phloem loading, density of loading veins, plasmodesmatal frequency in intermediary cells, and the ratio of l...
journal_title：Photosynthesis research
pub_type： 杂志文章,评审
doi：10.1007/s11120-006-9123-3
更新日期：2007-11-01 00:00:00
abstract：:The interaction of PsaC with the core heterodimer of Photosystem 1 was studied in wild type Synechocystis sp. PCC 6803 and the site-directed mutant R561E of PsaB. The mutant reaction center was much less stable in urea and the functional reconstitution of the mutant core using PsaC was impaired. However, the extent of...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/BF00018261
更新日期：1994-12-01 00:00:00
abstract：:Application of target theory to the photoinactivation of Photosystem II in pea leaf discs (Park et al. 1995, 1996a,b) reveals that there is a critical light dosage below which there is complete photoprotection and above which there is photoinactivation (i.e a light-induced loss of oxygen flash yield). The critical dos...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/BF00018219
更新日期：1996-10-01 00:00:00
abstract：:The problem of predicting the kinetics of proton efflux and the decay of the internal proton concentration for vesicles containing one or more buffers for which the internal proton concentration is initially higher than that of the surrounding medium is examined. An analytical solution is derived that describes the ti...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/BF00019150
更新日期：1987-01-01 00:00:00
abstract：:Rates of net CO2 uptake were examined in developing leaves of Hydrocotyle bonariensis. Leaves that developed under high photosynthetically active radiation (48 mol m(-2) day(-1) PAR) were smaller, thicker, and reached maximum size sooner than did leaves that developed under low PAR (4.8 mol m(-2) day(-1)). Maximum net...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/BF00028750
更新日期：1981-06-01 00:00:00
abstract：:The dependence on temperature of tryptophan fluorescence lifetime in trimeric photosystem I (PSI) complexes from cyanobacteria Synechocystis sp. PCC 6803 during the heating of pre-frozen to - 180 °C in the dark or in the light-activated preparations has been studied. Fluorescence lifetime in samples frozen in the ligh...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/s11120-018-0595-8
更新日期：2019-03-01 00:00:00
abstract：:Photosynthesis and carbohydrate metabolism of higher plants need to be tightly regulated to prevent tissue damage during environmental changes. The intracellular position of chloroplasts changes due to a changing light regime. Chloroplast avoidance and accumulation response under high and low light, respectively, are ...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/s11120-020-00795-y
更新日期：2021-01-01 00:00:00
abstract：:In plants, chlorophylls (chlorophyll a and chlorophyll b) are the most abundant tetrapyrrole molecules and are essential for photosynthesis. The first committed step of chlorophyll biosynthesis is the insertion of Mg(2+) into protoporphyrin IX, and thus subsequent steps of the biosynthesis are called the Mg branch. As...
journal_title：Photosynthesis research
pub_type： 杂志文章,评审
doi：10.1007/s11120-008-9291-4
更新日期：2008-05-01 00:00:00
abstract：:Sulphoquinovosyldiacylglycerol is a negatively charged lipid which exists in the thylakoid membrane. It is proposed that a large proportion of this acidic lipid does not form a part of the bulk lipid matrix but is closely associated with protein complexes where it is tightly bound and participates in either optimising...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/BF00029747
更新日期：1986-01-01 00:00:00
abstract：:Cyanobacteria are photosynthetic prokaryotes and widely used for photosynthetic research as model organisms. Partly due to their prokaryotic nature, however, estimation of photosynthesis by chlorophyll fluorescence measurements is sometimes problematic in cyanobacteria. For example, plastoquinone pool is reduced in th...
journal_title：Photosynthesis research
pub_type： 杂志文章,评审
doi：10.1007/s11120-017-0367-x
更新日期：2017-09-01 00:00:00
abstract：:The factors governing quinone protein binding in the photosynthetic bacterium Rps. viridis are investigated via use of empirical intermolecular energy calculations using the GRID method (PJ Goodford (1985) J Med Chem 28: 849-854). A probe atom corresponding to a carbonyl oxygen atom is used to investigate regions exhi...
journal_title：Photosynthesis research
pub_type： 杂志文章
doi：10.1007/BF00027142
更新日期：1994-01-01 00:00:00
