Saif Hasan | BRAC University (original) (raw)

Papers by Saif Hasan

modifications of integral membrane proteins resolved by top-down

Advances in Photosynthesis and Respiration, 2016

Structure-function studies of the cytochrome b 6 f complex, the central hetero-oligomeric membran... more Structure-function studies of the cytochrome b 6 f complex, the central hetero-oligomeric membrane protein complex in the electron transport chain of oxygenic photosynthesis, which formed the basis for a high-resolution (2.5 Å) crystallographic solution of the complex, are described. Structure-function differences between the structure of subunits of the bc complexes, b 6 f, and bc 1 from mitochondria and photosynthetic bacteria, which are often assumed to function identically, are discussed. Major differences which suggest that quinone-dependent electron transport pathways can vary in b 6 f and bc 1 complexes are as follows: (a) an additional c-type heme, c n , and bound single copies of chlorophyll a and β-carotene in the b 6 f complex; and (b) a cyclic electron transport pathway that encompasses the b 6 f and PSI reaction center complexes. The importance of including lipid in crystallization of the cytochrome complex, or with any hetero-oligomeric membrane protein complex, is emphasized, and consequences to structure-function of b 6 f being a lipoprotein complex discussed, including intra-protein dielectric heterogeneity and resultant pathways of trans-membrane electron transport. The role of the b 6 f complex in transmembrane signal transduction from reductant generated on the p-side of the electron transport chain to the regulation of light energy to the two photosystems by trans-side phosphorylation of the light-harvesting chlorophyll protein is presented. Regarding structure aspects relevant to plastoquinol-quinone entrance-egress: (i) modification of the p-side channel for plastoquinone access to the iron-sulfur protein would change the rate-limiting step in electron transport; (ii) the narrow niche for entry of plastoquinol into b 6 f from the PSII reaction center complex would seem to require close proximity between the complexes.

Biophysical Journal, 2014

Biophysical Journal, 2014

The cytochrome bc complexes b 6 f and bc 1 catalyze proton-coupled quinol/quinone redox reactions... more The cytochrome bc complexes b 6 f and bc 1 catalyze proton-coupled quinol/quinone redox reactions to generate a transmembrane proton electrochemical gradient. Quinol oxidation on the electrochemically positive (p) interface of the complex occurs at the end of a narrow quinol/quinone entry/exit Q p portal, 11 Å long in bc complexes. Superoxide, which has multiple signaling functions, is a by-product of the p-side quinol oxidation. Although the transmembrane core and the chemistry of quinone redox reactions are conserved in bc complexes, the rate of superoxide generation is an order of magnitude greater in the b 6 f complex, implying that functionally significant differences in structure exist between the b 6 f and bc 1 complexes on the p-side. A unique structure feature of the b 6 f p-side quinol oxidation site is the presence of a single chlorophyll-a molecule whose function is unrelated to light harvesting. This study describes a cocrystal structure of the cytochrome b 6 f complex with the quinol analog stigmatellin, which partitions in the Q p portal of the bc 1 complex, but not effectively in b 6 f. It is inferred that the Q p portal is partially occluded in the b 6 f complex relative to bc 1. Based on a discrete molecular-dynamics analysis, occlusion of the Q p portal is attributed to the presence of the chlorophyll phytyl tail, which increases the quinone residence time within the Q p portal and is inferred to be a cause of enhanced superoxide production. This study attributes a novel (to our knowledge), structurelinked function to the otherwise enigmatic chlorophyll-a in the b 6 f complex, which may also be relevant to intracellular redox signaling.

Current Protocols in Protein Science, 2013

Methods in Molecular Biology, 2010

Home > Purification and crystallization of the cyanobacterial cytochrome b6f complex. Purificatio... more Home > Purification and crystallization of the cyanobacterial cytochrome b6f complex. Purification and crystallization of the cyanobacterial cytochrome b6f complex.

The role of lipids in the assembly, structure, and function of hetero-oligomeric membrane protein... more The role of lipids in the assembly, structure, and function of hetero-oligomeric membrane protein complexes is poorly understood. The dimeric photosynthetic cytochrome b 6 f complex, a 16-mer of eight distinct subunits and 26 transmembrane helices, catalyzes transmembrane proton-coupled electron transfer for energy storage. Using a 2.5 Å crystal structure of the dimeric complex, we identified 23 distinct lipid-binding sites per monomer. Annular lipids are proposed to provide a connection for super-complex formation with the photosystem-I reaction center and the LHCII kinase enzyme for transmembrane signaling. Internal lipids mediate crosslinking to stabilize the domain-swapped ironsulfur protein subunit, dielectric heterogeneity within intermonomer and intramonomer electron transfer pathways, and dimer stabilization through lipid-mediated intermonomer interactions. This study provides a complete structure analysis of lipid-mediated functions in a multi-subunit membrane protein complex and reveals lipid sites at positions essential for assembly and function.

Proceedings of the 2nd ACM SIGKDD International Workshop on Urban Computing - UrbComp '13, 2013

Location-based check-in services enable individuals to share their activity-related choices provi... more Location-based check-in services enable individuals to share their activity-related choices providing a new source of human activity data for researchers. In this paper urban human mobility and activity patterns are analyzed using locationbased data collected from social media applications (e.g. Foursquare and Twitter). We first characterize aggregate activity patterns by finding the distributions of different activity categories over a city geography and thus determine the purpose-specific activity distribution maps. We then characterize individual activity patterns by finding the timing distribution of visiting different places depending on activity category. We also explore the frequency of visiting a place with respect to the rank of the place in individual's visitation records and show interesting match with the results from other studies based on mobile phone data.

Encyclopedia of Biological Chemistry, 2013

ABSTRACT Structure–function of the major integral membrane cytochrome b6f complex that functions ... more ABSTRACT Structure–function of the major integral membrane cytochrome b6f complex that functions in cyanobacteria, algae, and green plants to transfer electrons between the two reaction center complexes in the electron transport chain of oxygenic photosynthesis is discussed in the context of recently obtained crystal structures of the complex and soluble domains of cytochrome f and the Rieske iron–sulfur protein. The energy-transducing function of the complex, generation of the proton trans-membrane electrochemical potential gradient, centers on the oxidation/reduction pathways of the plastoquinol/plastoquinone (QH2/Q), the proton donor/acceptor within the complex. These redox reactions are carried out by five redox prosthetic groups embedded in each monomer, the high potential two iron–two sulfur cluster and the heme of cytochrome f on the electropositive side (p) of the complex, two noncovalently bound b-type hemes that cross the complex and the membrane, and a covalently bound c-type heme (cn) on the electronegative side (n). These five redox-active groups are organized in high- (cyt f/[2Fe–2S] and low-potential (hemes bp, bn, cn) electron transport pathways that oxidize and reduce the quinol and quinone on the p- and n-sides in a Q-cycle-type mechanism, while translocating as many as 2 H+ to the p-side aqueous side for every electron transferred through the high potential chain to the photosystem I reaction center. The presence of heme cn and the connection of the n-side of the membrane and b6f complex to the cyclic electron transport chain indicate that the Q cycle in the oxygenic photosynthetic electron transport chain differs from those connected to the bc1 complex in the mitochondrial respiratory chain and the chain in photosynthetic bacteria. Inferences from the structure and C2 symmetry of the complex for the pathway of QH2/Q transfer within the complex, problems posed by the presence of lipid in the inter-monomer cavity, and the narrow portal for QH2 passage through the p-side oxidation site proximal to the [2Fe–2S] cluster are discussed.

Proceedings of the National Academy of Sciences, 2013

As much as two-thirds of the proton gradient used for transmembrane free energy storage in oxygen... more As much as two-thirds of the proton gradient used for transmembrane free energy storage in oxygenic photosynthesis is generated by the cytochrome b 6 f complex. The proton uptake pathway from the electrochemically negative (n) aqueous phase to the n-side quinone binding site of the complex, and a probable route for proton exit to the positive phase resulting from quinol oxidation, are defined in a 2.70-Å crystal structure and in structures with quinone analog inhibitors at 3.07 Å (tridecyl-stigmatellin) and 3.25-Å (2-nonyl-4-hydroxyquinoline N-oxide) resolution. The simplest n-side proton pathway extends from the aqueous phase via Asp20 and Arg207 (cytochrome b 6 subunit) to quinone bound axially to heme c n . On the positive side, the heme-proximal Glu78 (subunit IV), which accepts protons from plastosemiquinone, defines a route for H + transfer to the aqueous phase. These pathways provide a structure-based description of the quinone-mediated proton transfer responsible for generat...

Journal of Biological Chemistry, 2009

The crystal structure of the cyanobacterial cytochrome b 6 f complex has previously been solved t... more The crystal structure of the cyanobacterial cytochrome b 6 f complex has previously been solved to 3.0-Å resolution using the thermophilic Mastigocladus laminosus whose genome has not been sequenced. Several unicellular cyanobacteria, whose genomes have been sequenced and are tractable for mutagenesis, do not yield b 6 f complex in an intact dimeric state with significant electron transport activity. The genome of Nostoc sp. PCC 7120 has been sequenced and is closer phylogenetically to M. laminosus than are unicellular cyanobacteria. The amino acid sequences of the large core subunits and four small peripheral subunits of Nostoc are 88 and 80% identical to those in the M. laminosus b 6 f complex. Purified b 6 f complex from Nostoc has a stable dimeric structure, eight subunits with masses similar to those of M. laminosus, and comparable electron transport activity. The crystal structure of the native b 6 f complex, determined to a resolution of 3.0 Å (PDB id: 2ZT9), is almost identical to that of M. laminosus. Two unique aspects of the Nostoc complex are: (i) a dominant conformation of heme b p that is rotated 180°a bout the ␣and ␥-meso carbon axis relative to the orientation in the M. laminosus complex and (ii) acetylation of the Rieske iron-sulfur protein (PetC) at the N terminus, a post-translational modification unprecedented in cyanobacterial membrane and electron transport proteins, and in polypeptides of cytochrome bc complexes from any source. The high spin electronic character of the unique heme c n is similar to that previously found in the b 6 f complex from other sources.

Biophysical Journal, 2012

Biophysical Journal, 2013

wild-type RBS COX; however, the a-region of the reduced spectrum for E90H(SIII) displayed a sligh... more wild-type RBS COX; however, the a-region of the reduced spectrum for E90H(SIII) displayed a slight red shift of the absorbance maximum by 1 nm, resembling that seen for the SIII-depleted oxidase. E90H(III) and E90H/ H212(III) mutant proteins were determined to contain stoichiometric amount of each subunit by SDS-PAGE gel, similar to wild-type COX. Electron transfer rates observed at pH 6.5, for E90H(III)/H212E(III) and E90H(SIII) COX, were decreased by 17 and 39% respectively, as compared to WT COX. The mutants exhibit little or no suicide inactivation when compared to the SIII-depleted RBS COX. pH dependence of electron transfer activity for E90H(III)/ H212E(III) and E90H(III) were also not altered when compared to WT enzyme. Proton pumping experiments on reconstituted E90H(III) and E90H(III)/ H212E(III) in liposomes will be discussed.

Biophysical Journal, 2013

wild-type RBS COX; however, the a-region of the reduced spectrum for E90H(SIII) displayed a sligh... more wild-type RBS COX; however, the a-region of the reduced spectrum for E90H(SIII) displayed a slight red shift of the absorbance maximum by 1 nm, resembling that seen for the SIII-depleted oxidase. E90H(III) and E90H/ H212(III) mutant proteins were determined to contain stoichiometric amount of each subunit by SDS-PAGE gel, similar to wild-type COX. Electron transfer rates observed at pH 6.5, for E90H(III)/H212E(III) and E90H(SIII) COX, were decreased by 17 and 39% respectively, as compared to WT COX. The mutants exhibit little or no suicide inactivation when compared to the SIII-depleted RBS COX. pH dependence of electron transfer activity for E90H(III)/ H212E(III) and E90H(III) were also not altered when compared to WT enzyme. Proton pumping experiments on reconstituted E90H(III) and E90H(III)/ H212E(III) in liposomes will be discussed.

Biophysical Journal, 2011

mechanism was still unrevealed. We demonstrate a new, conserved actin binding region, called acti... more mechanism was still unrevealed. We demonstrate a new, conserved actin binding region, called activation loop. It is located at the relay region which swings the lever of myosin upon the powerstroke. We prove that activation loop interacts with the N-terminal segment of actin. We found that this interaction specifically activates myosin ATPase. Biochemical (steady state and transient kinetic fluorescent measurements) and in vivo experiments using transgenic C. elegans strains proved that activation loop is responsible for force production but not essential for motility per se. We conclude that actin binding to activation loop directly accelerates the lever movement. This process increases the ratio of working myosin heads and produce effective muscle contraction. 706-Pos Board B506 Interaction of a Novel Fluorescent Non-Nucleotide ATP Analogue with ATP-Driven Molecular Motors Keiko Tanaka, Taro Kimura, Shinsaku Maruta. Fluorescent nucleotide analogues are essential for analysis of nucleotide-binding proteins. Most of fluorescent-labeled ATP analogues are ribose-modified. However, they are known to be 2' and 3' isomers mixture. Often these isomers show different properties each other. To avoid isomers, we designed and synthesized non-nucleotide fluorescent ATP-analogue, N-methylanthraniloyl amino ethyl triphosphate (MANTTP) which similar structure to the non-nucleotide ATP analogue 2-[(4-azido-2-nitrophenyl) amino] ethyl triphosphate (NANTP). It is known that NANTP are good substrate for skeletal myosin and induces actin gliding in vitro motility assay. Excitation and emission maximums in the fluorescence spectrum MANTTP were 330nm and 430nm, respectively. MANTTP was hydrolyzed by conventional kinesin and skeletal myosin, and induced dissociation of acto-myosin. The MANTTPase of myosin and kinesin were significantly activated by actin and microtubule, respectively. The ADP form of MANTTP showed the formation of skeletal muscle myosin-MANTDP-BeFn complex which mimic the transient state in ATPase cycle and this complex detaches from actin filament. K SV of MANTDP-S-1-phosphate analogue complex showed significantly smaller value than that of free MANTTP. The results suggested that the fluorophore moiety of MANTDP in the complex is buried deeply in the ATP binding site. The fluorescent intensity of MANTTP itself does not change on binding to myosin ATP binding site, however, MANTTP showed significant FRET between intrinsic tryptophan residue of skeletal muscle myosin and MANTTP. The binding of MANTTP to myosin can be observed as fluorescence increase on the stopped flow system. The second-order rate constant for MANTTP first binding to myosin is 0.15Â10 À6 M À1 s À1. It was shown that the novel fluorescent ATP analogue is applicable to the kinetic studies on ATPases.

Biophysical Journal, 2011

Biochemistry, 2013

Cytochrome b 6 f catalyzes quinone redox reactions within photosynthetic membranes to generate a ... more Cytochrome b 6 f catalyzes quinone redox reactions within photosynthetic membranes to generate a transmembrane proton electrochemical gradient for ATP synthesis. A key step involves the transfer of an electron from the [2Fe-2S] cluster of the iron−sulfur protein (ISP) extrinsic domain to the cytochrome f heme across a distance of 26 Å, which is too large for competent electron transfer but could be bridged by translation−rotation of the ISP. Here we report the first crystallographic evidence of significant motion of the ISP extrinsic domain. It is inferred that extensive crystallographic disorder of the ISP extrinsic domain indicates conformational flexibility. The ISP disorder observed in this structure, in contrast to the largely ordered ISP structure observed in the b 6 f complex supplemented with neutral lipids, is attributed to electrostatic interactions arising from anionic lipids.

Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2011

Cytochrome bc 1 /b 6 f complex Electron transfer Energy transduction Plasto-/ubiquinone Electroch... more Cytochrome bc 1 /b 6 f complex Electron transfer Energy transduction Plasto-/ubiquinone Electrochemical potential Aspects of the crystal structures of the hetero-oligomeric cytochrome bc 1 and b 6 f ("bc") complexes relevant to their electron/proton transfer function and the associated redox reactions of the lipophilic quinones are discussed. Differences between the b 6 f and bc 1 complexes are emphasized. The cytochrome bc 1 and b 6 f dimeric complexes diverge in structure from a core of subunits that coordinate redox groups consisting of two bis-histidine coordinated hemes, a heme b n and b p on the electrochemically negative (n) and positive (p) sides of the complex, the high potential [2Fe-2S] cluster and c-type heme at the p-side aqueous interface and aqueous phase, respectively, and quinone/quinol binding sites on the n-and p-sides of the complex. The bc 1 and b 6 f complexes diverge in subunit composition and structure away from this core. b 6 f Also contains additional prosthetic groups including a c-type heme c n on the n-side, and a chlorophyll a and β-carotene. Common structure aspects; functions of the symmetric dimer. (I) Quinone exchange with the bilayer. An inter-monomer protein-free cavity of approximately 30 Å along the membrane normal×25 Å (central inter-monomer distance)× 15 Å (depth in the center), is common to both bc 1 and b 6 f complexes, providing a niche in which the lipophilic quinone/quinol (Q/QH 2) can be exchanged with the membrane bilayer. (II) Electron transfer. The dimeric structure and the proximity of the two hemes b p on the electrochemically positive side of the complex in the two monomer units allow the possibility of two alternate routes of electron transfer across the complex from heme b p to b n : intra-monomer and inter-monomer involving electron cross-over between the two hemes b p. A structure-based summary of inter-heme distances in seven bc complexes, representing mitochondrial, chromatophore, cyanobacterial, and algal sources, indicates that, based on the distance parameter, the intra-monomer pathway would be favored kinetically. (III) Separation of quinone binding sites. A consequence of the dimer structure and the position of the Q/QH 2 binding sites is that the p-side QH 2 oxidation and n-side Q reduction sites are each well separated. Therefore, in the event of an overlap in residence time by QH 2 or Q molecules at the two oxidation or reduction sites, their spatial separation would result in minimal steric interference between extended Q or QH 2 isoprenoid chains. (IV) Trans-membrane QH 2 /Q transfer. (i) n/p-side QH 2 /Q transfer may be hindered by lipid acyl chains; (ii) the shorter less hindered inter-monomer pathway across the complex would not pass through the center of the cavity, as inferred from the n-side antimycin site on one monomer and the p-side stigmatellin site on the other residing on the same surface of the complex. (V) Narrow p-side portal for QH 2 /Q passage. The [2Fe-2S] cluster that serves as oxidant, and whose histidine ligand serves as a H + acceptor in the oxidation of QH 2 , is connected to the inter-monomer cavity by a narrow extended portal, which is also occupied in the b 6 f complex by the 20 carbon phytyl chain of the bound chlorophyll.

Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2013

Structure-function properties of the cytochrome b 6 f complex are sufficiently unique compared to... more Structure-function properties of the cytochrome b 6 f complex are sufficiently unique compared to those of the cytochrome bc 1 complex that b 6 f should not be considered a trivially modified bc 1 complex. A unique property of the dimeric b 6 f complex is its involvement in transmembrane signaling associated with the p-side oxidation of plastoquinol. Structure analysis of lipid binding sites in the cyanobacterial b 6 f complex prepared by hydrophobic chromatography shows that the space occupied by the H transmembrane helix in the cytochrome b subunit of the bc 1 complex is mostly filled by a lipid in the b 6 f crystal structure. It is suggested that this space can be filled by the domain of a transmembrane signaling protein. The identification of lipid sites and likely function defines the intra-membrane conserved central core of the b 6 f complex, consisting of the seven trans-membrane helices of the cytochrome b and subunit IV polypeptides. The other six TM helices, contributed by cytochrome f, the iron-sulfur protein, and the four peripheral single span subunits, define a peripheral less conserved domain of the complex. The distribution of conserved and non-conserved domains of each monomer of the complex, and the position and inferred function of a number of the lipids, suggests a model for the sequential assembly in the membrane of the eight subunits of the b 6 f complex, in which the assembly is initiated by formation of the cytochrome b 6-subunit IV core sub-complex in a monomer unit. Two conformations of the unique lipidic chlorophyll a, defined in crystal structures, are described, and functions of the outlying β-carotene, a possible 'latch' in supercomplex formation, are discussed. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.

modifications of integral membrane proteins resolved by top-down

Advances in Photosynthesis and Respiration, 2016

Structure-function studies of the cytochrome b 6 f complex, the central hetero-oligomeric membran... more Structure-function studies of the cytochrome b 6 f complex, the central hetero-oligomeric membrane protein complex in the electron transport chain of oxygenic photosynthesis, which formed the basis for a high-resolution (2.5 Å) crystallographic solution of the complex, are described. Structure-function differences between the structure of subunits of the bc complexes, b 6 f, and bc 1 from mitochondria and photosynthetic bacteria, which are often assumed to function identically, are discussed. Major differences which suggest that quinone-dependent electron transport pathways can vary in b 6 f and bc 1 complexes are as follows: (a) an additional c-type heme, c n , and bound single copies of chlorophyll a and β-carotene in the b 6 f complex; and (b) a cyclic electron transport pathway that encompasses the b 6 f and PSI reaction center complexes. The importance of including lipid in crystallization of the cytochrome complex, or with any hetero-oligomeric membrane protein complex, is emphasized, and consequences to structure-function of b 6 f being a lipoprotein complex discussed, including intra-protein dielectric heterogeneity and resultant pathways of trans-membrane electron transport. The role of the b 6 f complex in transmembrane signal transduction from reductant generated on the p-side of the electron transport chain to the regulation of light energy to the two photosystems by trans-side phosphorylation of the light-harvesting chlorophyll protein is presented. Regarding structure aspects relevant to plastoquinol-quinone entrance-egress: (i) modification of the p-side channel for plastoquinone access to the iron-sulfur protein would change the rate-limiting step in electron transport; (ii) the narrow niche for entry of plastoquinol into b 6 f from the PSII reaction center complex would seem to require close proximity between the complexes.

Biophysical Journal, 2014

Biophysical Journal, 2014

The cytochrome bc complexes b 6 f and bc 1 catalyze proton-coupled quinol/quinone redox reactions... more The cytochrome bc complexes b 6 f and bc 1 catalyze proton-coupled quinol/quinone redox reactions to generate a transmembrane proton electrochemical gradient. Quinol oxidation on the electrochemically positive (p) interface of the complex occurs at the end of a narrow quinol/quinone entry/exit Q p portal, 11 Å long in bc complexes. Superoxide, which has multiple signaling functions, is a by-product of the p-side quinol oxidation. Although the transmembrane core and the chemistry of quinone redox reactions are conserved in bc complexes, the rate of superoxide generation is an order of magnitude greater in the b 6 f complex, implying that functionally significant differences in structure exist between the b 6 f and bc 1 complexes on the p-side. A unique structure feature of the b 6 f p-side quinol oxidation site is the presence of a single chlorophyll-a molecule whose function is unrelated to light harvesting. This study describes a cocrystal structure of the cytochrome b 6 f complex with the quinol analog stigmatellin, which partitions in the Q p portal of the bc 1 complex, but not effectively in b 6 f. It is inferred that the Q p portal is partially occluded in the b 6 f complex relative to bc 1. Based on a discrete molecular-dynamics analysis, occlusion of the Q p portal is attributed to the presence of the chlorophyll phytyl tail, which increases the quinone residence time within the Q p portal and is inferred to be a cause of enhanced superoxide production. This study attributes a novel (to our knowledge), structurelinked function to the otherwise enigmatic chlorophyll-a in the b 6 f complex, which may also be relevant to intracellular redox signaling.

Current Protocols in Protein Science, 2013

Methods in Molecular Biology, 2010

Home > Purification and crystallization of the cyanobacterial cytochrome b6f complex. Purificatio... more Home > Purification and crystallization of the cyanobacterial cytochrome b6f complex. Purification and crystallization of the cyanobacterial cytochrome b6f complex.

The role of lipids in the assembly, structure, and function of hetero-oligomeric membrane protein... more The role of lipids in the assembly, structure, and function of hetero-oligomeric membrane protein complexes is poorly understood. The dimeric photosynthetic cytochrome b 6 f complex, a 16-mer of eight distinct subunits and 26 transmembrane helices, catalyzes transmembrane proton-coupled electron transfer for energy storage. Using a 2.5 Å crystal structure of the dimeric complex, we identified 23 distinct lipid-binding sites per monomer. Annular lipids are proposed to provide a connection for super-complex formation with the photosystem-I reaction center and the LHCII kinase enzyme for transmembrane signaling. Internal lipids mediate crosslinking to stabilize the domain-swapped ironsulfur protein subunit, dielectric heterogeneity within intermonomer and intramonomer electron transfer pathways, and dimer stabilization through lipid-mediated intermonomer interactions. This study provides a complete structure analysis of lipid-mediated functions in a multi-subunit membrane protein complex and reveals lipid sites at positions essential for assembly and function.

Proceedings of the 2nd ACM SIGKDD International Workshop on Urban Computing - UrbComp '13, 2013

Location-based check-in services enable individuals to share their activity-related choices provi... more Location-based check-in services enable individuals to share their activity-related choices providing a new source of human activity data for researchers. In this paper urban human mobility and activity patterns are analyzed using locationbased data collected from social media applications (e.g. Foursquare and Twitter). We first characterize aggregate activity patterns by finding the distributions of different activity categories over a city geography and thus determine the purpose-specific activity distribution maps. We then characterize individual activity patterns by finding the timing distribution of visiting different places depending on activity category. We also explore the frequency of visiting a place with respect to the rank of the place in individual's visitation records and show interesting match with the results from other studies based on mobile phone data.

Encyclopedia of Biological Chemistry, 2013

ABSTRACT Structure–function of the major integral membrane cytochrome b6f complex that functions ... more ABSTRACT Structure–function of the major integral membrane cytochrome b6f complex that functions in cyanobacteria, algae, and green plants to transfer electrons between the two reaction center complexes in the electron transport chain of oxygenic photosynthesis is discussed in the context of recently obtained crystal structures of the complex and soluble domains of cytochrome f and the Rieske iron–sulfur protein. The energy-transducing function of the complex, generation of the proton trans-membrane electrochemical potential gradient, centers on the oxidation/reduction pathways of the plastoquinol/plastoquinone (QH2/Q), the proton donor/acceptor within the complex. These redox reactions are carried out by five redox prosthetic groups embedded in each monomer, the high potential two iron–two sulfur cluster and the heme of cytochrome f on the electropositive side (p) of the complex, two noncovalently bound b-type hemes that cross the complex and the membrane, and a covalently bound c-type heme (cn) on the electronegative side (n). These five redox-active groups are organized in high- (cyt f/[2Fe–2S] and low-potential (hemes bp, bn, cn) electron transport pathways that oxidize and reduce the quinol and quinone on the p- and n-sides in a Q-cycle-type mechanism, while translocating as many as 2 H+ to the p-side aqueous side for every electron transferred through the high potential chain to the photosystem I reaction center. The presence of heme cn and the connection of the n-side of the membrane and b6f complex to the cyclic electron transport chain indicate that the Q cycle in the oxygenic photosynthetic electron transport chain differs from those connected to the bc1 complex in the mitochondrial respiratory chain and the chain in photosynthetic bacteria. Inferences from the structure and C2 symmetry of the complex for the pathway of QH2/Q transfer within the complex, problems posed by the presence of lipid in the inter-monomer cavity, and the narrow portal for QH2 passage through the p-side oxidation site proximal to the [2Fe–2S] cluster are discussed.

Proceedings of the National Academy of Sciences, 2013

As much as two-thirds of the proton gradient used for transmembrane free energy storage in oxygen... more As much as two-thirds of the proton gradient used for transmembrane free energy storage in oxygenic photosynthesis is generated by the cytochrome b 6 f complex. The proton uptake pathway from the electrochemically negative (n) aqueous phase to the n-side quinone binding site of the complex, and a probable route for proton exit to the positive phase resulting from quinol oxidation, are defined in a 2.70-Å crystal structure and in structures with quinone analog inhibitors at 3.07 Å (tridecyl-stigmatellin) and 3.25-Å (2-nonyl-4-hydroxyquinoline N-oxide) resolution. The simplest n-side proton pathway extends from the aqueous phase via Asp20 and Arg207 (cytochrome b 6 subunit) to quinone bound axially to heme c n . On the positive side, the heme-proximal Glu78 (subunit IV), which accepts protons from plastosemiquinone, defines a route for H + transfer to the aqueous phase. These pathways provide a structure-based description of the quinone-mediated proton transfer responsible for generat...

Journal of Biological Chemistry, 2009

The crystal structure of the cyanobacterial cytochrome b 6 f complex has previously been solved t... more The crystal structure of the cyanobacterial cytochrome b 6 f complex has previously been solved to 3.0-Å resolution using the thermophilic Mastigocladus laminosus whose genome has not been sequenced. Several unicellular cyanobacteria, whose genomes have been sequenced and are tractable for mutagenesis, do not yield b 6 f complex in an intact dimeric state with significant electron transport activity. The genome of Nostoc sp. PCC 7120 has been sequenced and is closer phylogenetically to M. laminosus than are unicellular cyanobacteria. The amino acid sequences of the large core subunits and four small peripheral subunits of Nostoc are 88 and 80% identical to those in the M. laminosus b 6 f complex. Purified b 6 f complex from Nostoc has a stable dimeric structure, eight subunits with masses similar to those of M. laminosus, and comparable electron transport activity. The crystal structure of the native b 6 f complex, determined to a resolution of 3.0 Å (PDB id: 2ZT9), is almost identical to that of M. laminosus. Two unique aspects of the Nostoc complex are: (i) a dominant conformation of heme b p that is rotated 180°a bout the ␣and ␥-meso carbon axis relative to the orientation in the M. laminosus complex and (ii) acetylation of the Rieske iron-sulfur protein (PetC) at the N terminus, a post-translational modification unprecedented in cyanobacterial membrane and electron transport proteins, and in polypeptides of cytochrome bc complexes from any source. The high spin electronic character of the unique heme c n is similar to that previously found in the b 6 f complex from other sources.

Biophysical Journal, 2012

Biophysical Journal, 2013

wild-type RBS COX; however, the a-region of the reduced spectrum for E90H(SIII) displayed a sligh... more wild-type RBS COX; however, the a-region of the reduced spectrum for E90H(SIII) displayed a slight red shift of the absorbance maximum by 1 nm, resembling that seen for the SIII-depleted oxidase. E90H(III) and E90H/ H212(III) mutant proteins were determined to contain stoichiometric amount of each subunit by SDS-PAGE gel, similar to wild-type COX. Electron transfer rates observed at pH 6.5, for E90H(III)/H212E(III) and E90H(SIII) COX, were decreased by 17 and 39% respectively, as compared to WT COX. The mutants exhibit little or no suicide inactivation when compared to the SIII-depleted RBS COX. pH dependence of electron transfer activity for E90H(III)/ H212E(III) and E90H(III) were also not altered when compared to WT enzyme. Proton pumping experiments on reconstituted E90H(III) and E90H(III)/ H212E(III) in liposomes will be discussed.

Biophysical Journal, 2013

wild-type RBS COX; however, the a-region of the reduced spectrum for E90H(SIII) displayed a sligh... more wild-type RBS COX; however, the a-region of the reduced spectrum for E90H(SIII) displayed a slight red shift of the absorbance maximum by 1 nm, resembling that seen for the SIII-depleted oxidase. E90H(III) and E90H/ H212(III) mutant proteins were determined to contain stoichiometric amount of each subunit by SDS-PAGE gel, similar to wild-type COX. Electron transfer rates observed at pH 6.5, for E90H(III)/H212E(III) and E90H(SIII) COX, were decreased by 17 and 39% respectively, as compared to WT COX. The mutants exhibit little or no suicide inactivation when compared to the SIII-depleted RBS COX. pH dependence of electron transfer activity for E90H(III)/ H212E(III) and E90H(III) were also not altered when compared to WT enzyme. Proton pumping experiments on reconstituted E90H(III) and E90H(III)/ H212E(III) in liposomes will be discussed.

Biophysical Journal, 2011

mechanism was still unrevealed. We demonstrate a new, conserved actin binding region, called acti... more mechanism was still unrevealed. We demonstrate a new, conserved actin binding region, called activation loop. It is located at the relay region which swings the lever of myosin upon the powerstroke. We prove that activation loop interacts with the N-terminal segment of actin. We found that this interaction specifically activates myosin ATPase. Biochemical (steady state and transient kinetic fluorescent measurements) and in vivo experiments using transgenic C. elegans strains proved that activation loop is responsible for force production but not essential for motility per se. We conclude that actin binding to activation loop directly accelerates the lever movement. This process increases the ratio of working myosin heads and produce effective muscle contraction. 706-Pos Board B506 Interaction of a Novel Fluorescent Non-Nucleotide ATP Analogue with ATP-Driven Molecular Motors Keiko Tanaka, Taro Kimura, Shinsaku Maruta. Fluorescent nucleotide analogues are essential for analysis of nucleotide-binding proteins. Most of fluorescent-labeled ATP analogues are ribose-modified. However, they are known to be 2' and 3' isomers mixture. Often these isomers show different properties each other. To avoid isomers, we designed and synthesized non-nucleotide fluorescent ATP-analogue, N-methylanthraniloyl amino ethyl triphosphate (MANTTP) which similar structure to the non-nucleotide ATP analogue 2-[(4-azido-2-nitrophenyl) amino] ethyl triphosphate (NANTP). It is known that NANTP are good substrate for skeletal myosin and induces actin gliding in vitro motility assay. Excitation and emission maximums in the fluorescence spectrum MANTTP were 330nm and 430nm, respectively. MANTTP was hydrolyzed by conventional kinesin and skeletal myosin, and induced dissociation of acto-myosin. The MANTTPase of myosin and kinesin were significantly activated by actin and microtubule, respectively. The ADP form of MANTTP showed the formation of skeletal muscle myosin-MANTDP-BeFn complex which mimic the transient state in ATPase cycle and this complex detaches from actin filament. K SV of MANTDP-S-1-phosphate analogue complex showed significantly smaller value than that of free MANTTP. The results suggested that the fluorophore moiety of MANTDP in the complex is buried deeply in the ATP binding site. The fluorescent intensity of MANTTP itself does not change on binding to myosin ATP binding site, however, MANTTP showed significant FRET between intrinsic tryptophan residue of skeletal muscle myosin and MANTTP. The binding of MANTTP to myosin can be observed as fluorescence increase on the stopped flow system. The second-order rate constant for MANTTP first binding to myosin is 0.15Â10 À6 M À1 s À1. It was shown that the novel fluorescent ATP analogue is applicable to the kinetic studies on ATPases.

Biophysical Journal, 2011

Biochemistry, 2013

Cytochrome b 6 f catalyzes quinone redox reactions within photosynthetic membranes to generate a ... more Cytochrome b 6 f catalyzes quinone redox reactions within photosynthetic membranes to generate a transmembrane proton electrochemical gradient for ATP synthesis. A key step involves the transfer of an electron from the [2Fe-2S] cluster of the iron−sulfur protein (ISP) extrinsic domain to the cytochrome f heme across a distance of 26 Å, which is too large for competent electron transfer but could be bridged by translation−rotation of the ISP. Here we report the first crystallographic evidence of significant motion of the ISP extrinsic domain. It is inferred that extensive crystallographic disorder of the ISP extrinsic domain indicates conformational flexibility. The ISP disorder observed in this structure, in contrast to the largely ordered ISP structure observed in the b 6 f complex supplemented with neutral lipids, is attributed to electrostatic interactions arising from anionic lipids.

Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2011

Cytochrome bc 1 /b 6 f complex Electron transfer Energy transduction Plasto-/ubiquinone Electroch... more Cytochrome bc 1 /b 6 f complex Electron transfer Energy transduction Plasto-/ubiquinone Electrochemical potential Aspects of the crystal structures of the hetero-oligomeric cytochrome bc 1 and b 6 f ("bc") complexes relevant to their electron/proton transfer function and the associated redox reactions of the lipophilic quinones are discussed. Differences between the b 6 f and bc 1 complexes are emphasized. The cytochrome bc 1 and b 6 f dimeric complexes diverge in structure from a core of subunits that coordinate redox groups consisting of two bis-histidine coordinated hemes, a heme b n and b p on the electrochemically negative (n) and positive (p) sides of the complex, the high potential [2Fe-2S] cluster and c-type heme at the p-side aqueous interface and aqueous phase, respectively, and quinone/quinol binding sites on the n-and p-sides of the complex. The bc 1 and b 6 f complexes diverge in subunit composition and structure away from this core. b 6 f Also contains additional prosthetic groups including a c-type heme c n on the n-side, and a chlorophyll a and β-carotene. Common structure aspects; functions of the symmetric dimer. (I) Quinone exchange with the bilayer. An inter-monomer protein-free cavity of approximately 30 Å along the membrane normal×25 Å (central inter-monomer distance)× 15 Å (depth in the center), is common to both bc 1 and b 6 f complexes, providing a niche in which the lipophilic quinone/quinol (Q/QH 2) can be exchanged with the membrane bilayer. (II) Electron transfer. The dimeric structure and the proximity of the two hemes b p on the electrochemically positive side of the complex in the two monomer units allow the possibility of two alternate routes of electron transfer across the complex from heme b p to b n : intra-monomer and inter-monomer involving electron cross-over between the two hemes b p. A structure-based summary of inter-heme distances in seven bc complexes, representing mitochondrial, chromatophore, cyanobacterial, and algal sources, indicates that, based on the distance parameter, the intra-monomer pathway would be favored kinetically. (III) Separation of quinone binding sites. A consequence of the dimer structure and the position of the Q/QH 2 binding sites is that the p-side QH 2 oxidation and n-side Q reduction sites are each well separated. Therefore, in the event of an overlap in residence time by QH 2 or Q molecules at the two oxidation or reduction sites, their spatial separation would result in minimal steric interference between extended Q or QH 2 isoprenoid chains. (IV) Trans-membrane QH 2 /Q transfer. (i) n/p-side QH 2 /Q transfer may be hindered by lipid acyl chains; (ii) the shorter less hindered inter-monomer pathway across the complex would not pass through the center of the cavity, as inferred from the n-side antimycin site on one monomer and the p-side stigmatellin site on the other residing on the same surface of the complex. (V) Narrow p-side portal for QH 2 /Q passage. The [2Fe-2S] cluster that serves as oxidant, and whose histidine ligand serves as a H + acceptor in the oxidation of QH 2 , is connected to the inter-monomer cavity by a narrow extended portal, which is also occupied in the b 6 f complex by the 20 carbon phytyl chain of the bound chlorophyll.

Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2013

Structure-function properties of the cytochrome b 6 f complex are sufficiently unique compared to... more Structure-function properties of the cytochrome b 6 f complex are sufficiently unique compared to those of the cytochrome bc 1 complex that b 6 f should not be considered a trivially modified bc 1 complex. A unique property of the dimeric b 6 f complex is its involvement in transmembrane signaling associated with the p-side oxidation of plastoquinol. Structure analysis of lipid binding sites in the cyanobacterial b 6 f complex prepared by hydrophobic chromatography shows that the space occupied by the H transmembrane helix in the cytochrome b subunit of the bc 1 complex is mostly filled by a lipid in the b 6 f crystal structure. It is suggested that this space can be filled by the domain of a transmembrane signaling protein. The identification of lipid sites and likely function defines the intra-membrane conserved central core of the b 6 f complex, consisting of the seven trans-membrane helices of the cytochrome b and subunit IV polypeptides. The other six TM helices, contributed by cytochrome f, the iron-sulfur protein, and the four peripheral single span subunits, define a peripheral less conserved domain of the complex. The distribution of conserved and non-conserved domains of each monomer of the complex, and the position and inferred function of a number of the lipids, suggests a model for the sequential assembly in the membrane of the eight subunits of the b 6 f complex, in which the assembly is initiated by formation of the cytochrome b 6-subunit IV core sub-complex in a monomer unit. Two conformations of the unique lipidic chlorophyll a, defined in crystal structures, are described, and functions of the outlying β-carotene, a possible 'latch' in supercomplex formation, are discussed. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.