Journal:

Article Title: Altered aggregation properties of mutant ?-crystallins cause inherited cataract

doi: 10.1093/emboj/cdf609

Figure Lengend Snippet: Fig. 3. α-crystallin prevents Crygbnop aggregation in vitro. (A) Recombinant γBnop-crystallin (red chromatogram) elutes in the void volume of a BioSec size exclusion column indicating aggregation to a size significantly bigger than the molecular weight of the monomeric protein (∼20 kDa). α-crystallin (black chromatogram), which oligomerizes in vivo to form particles of 800 kDa, elutes after the γBnop- crystallin peak. Wild-type mouse γ-crystallins and α-crystallins elute independently when separated on the same column (blue chromatogram): the γ-crystallins elute after 148 min, equivalent to their mol. wt of 20 kDa, whereas the α-crystallins elute at 91 min. When purified γBnop-crystallin was mixed in equimolar amounts with α-crystallin, two peaks were observed (green chromatogram). One peak has an equivalent elution time to α-crystallin, whilst the other peak is slightly smaller and shifted from the position seen for γBnop-crystallin alone (major peak in the red chromatogram). OD values have been adjusted relative to those obtained for α-crystallin to allow overlay of the different chromatograms. (B) The protein content of the two peaks from the green chromatogram was determined by SDS–PAGE, and each peak contains both α-crystallin (α) and γBnop-crystallin (N). This shows that γBnop-crystallin and α-crystallins co-elute, indicating that a protein complex has formed between these proteins. Proteins in fractions after 70, 72, 78, 82, 86, 90, 94 and 98 min are shown in tracks 1–8, respectively. Track M contains marker proteins of 30, 17.2 and 12.3 kDa, indicated by dots. The purity of the starting material γBnop-crystallin is shown (track Nop).

Article Snippet: These data support a role for α-crystallins by possibly preventing the formation of cytoplasmic aggregates by γB nop -crystallin and the other mutated γ-crystallins, leaving the nuclear deposits as the characteristic histopathological feature. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window caption a7 Fig. 3. α-crystallin prevents Crygb nop aggregation in vitro . ( A ) Recombinant γB nop -crystallin (red chromatogram) elutes in the void volume of a BioSec size exclusion column indicating aggregation to a size significantly bigger than the molecular weight of the monomeric protein (∼20 kDa). α-crystallin (black chromatogram), which oligomerizes in vivo to form particles of 800 kDa, elutes after the γB nop - crystallin peak.

Techniques: In Vitro, Recombinant, Molecular Weight, In Vivo, Purification, SDS Page, Marker

Journal: The Journal of Biological Chemistry

Article Title: Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn -Glycerol-1-phosphate Dehydrogenase *

doi: 10.1074/jbc.M115.647461

Figure Lengend Snippet: Top structural alignment hits from the Dali-based structural alignment of MJ G1PDH ( 36 ) MR, maleylacetate reductase; POR, 1,3-propanediol oxidoreductase.

Article Snippet: Previous biochemical characterizations of archaeal G1PDHs have shown the enzyme to be multimeric ( 17 , 42 ). table ft1 table-wrap mode="anchored" t5 TABLE 3 caption a7 Organism Class Protein Data Bank code-monomer Z-score a r.m.s.d. b lali c %id d C. acetobutylicum ATCC 824 GDH 3CE9-A 39.1 2.0 310 34 Sinorhizobium meliloti GDH 3UHJ-A 31.7 2.6 305 21 Geobacillus stearothermophilus GDH 1JQ5-A 30.3 2.5 300 21 Serratia plymuthica A30 GDH 4MCA-A 30.1 2.7 302 21 Schizosaccharomyces pombe GDH 1TA9-B 29.7 2.7 306 20 T. maritima GDH 1KQ3-A 29.5 2.6 301 26 E. coli Lactaldehyde reductase 1RRM-A 27.2 3.1 301 16 Ralstonia eutropha Fe-ADH 3JZD-A 26.9 2.9 302 15 Rhizobium sp. MTP-10005 MR 3W5S-A 26.8 3.2 300 15 Klebsiella pneumoniae POR 3BFJ-A 26.7 3.1 302 18 Agrobacterium tumefaciens MR 3HL0-A 26.8 3.0 302 15 Zymomonas mobilis ADH 2 3OWO-A 26.4 3.2 302 16 O. oeni POR 4FR2-A 26.4 3.2 302 20 Corynebacterium glutamicum ADH IV 3IV7-A 26.0 3.1 303 16 T. maritima Butanol dehydrogenase 1VLJ-B 25.2 3.5 299 18 T. maritima Fe-ADH 1VHD-A 25.1 3.2 294 18 Geobacillus thermoglucosidasius ADH 3ZDR-A 24.2 3.2 299 16 Shewanella denitrificans Fe-ADH 3RF7-A 24.2 3.4 290 17 E. coli Hypothetical oxidoreductase YqhD 1OJ7-A 23.6 3.9 300 17 Actinidia chinensis DHQS 3ZOK-D 23.0 3.5 294 16 Mycobacterium tuberculosis DHQS 3QBE-A 22.9 2.9 287 14 Aspergillus nidulans DHQS 1NVB-B 22.3 3.3 290 17 Streptomyces hygroscopicus Cyclase 4P53-A 21.0 2.9 277 16 Staphylococcus aureus DHQS 1XAG-A 20.9 3.3 282 17 Bacillus circulans 2-Deoxy- scyllo -inosose synthase 2GRU-A 20.3 3.2 283 18 Staphylococcus aureus DHQS 1XAH-A 19.5 3.2 264 16 Vibrio cholerae DHQS 3OKF-A 19.4 3.4 280 18 T. thermophilus DHQS 1UJN-A 18.8 3.4 271 14 Helicobacter pylori DHQS 3CLH-A 17.6 3.4 255 21 Open in a separate window a A measure of the statistical significance of the result relative to an alignment of random structures. b Root mean square deviation of α-carbon atoms. c Number of aligned residues. d Sequence identity between the two chains.

Techniques:

Journal: The Journal of Biological Chemistry

Article Title: Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn -Glycerol-1-phosphate Dehydrogenase *

doi: 10.1074/jbc.M115.647461

Figure Lengend Snippet: Expanded gap version of Dali-lite pairwise structural alignment of MJ G1PDH (36). Selected members of the larger enzyme superfamily including GDHs (Protein Data Bank codes 3CE9 and 1JQ5), ADHs (Protein Data Bank codes 1RRM, 3JZD, 3BFJ, and 4FR2), and DHQSs (Protein Data Bank codes 3QBE, 1XAG, and 1UJN) were used in the alignment. Secondary structural elements and residue numbering correspond to G1PDH. Residues that coordinate metals are highlighted in blue. The coenzyme binding motif is in italics, whereas residues that interact with coenzyme (NADP(H)) and substrate (DHAP) with respect to MJ G1PDH are highlighted in yellow and green, respectively. Reported intersubunit contacts between monomers are in red. Uppercase lettering indicates structurally equivalent positions with G1PDH, whereas lowercase indicates insertions relative to G1PDH.

Article Snippet: Previous biochemical characterizations of archaeal G1PDHs have shown the enzyme to be multimeric ( 17 , 42 ). table ft1 table-wrap mode="anchored" t5 TABLE 3 caption a7 Organism Class Protein Data Bank code-monomer Z-score a r.m.s.d. b lali c %id d C. acetobutylicum ATCC 824 GDH 3CE9-A 39.1 2.0 310 34 Sinorhizobium meliloti GDH 3UHJ-A 31.7 2.6 305 21 Geobacillus stearothermophilus GDH 1JQ5-A 30.3 2.5 300 21 Serratia plymuthica A30 GDH 4MCA-A 30.1 2.7 302 21 Schizosaccharomyces pombe GDH 1TA9-B 29.7 2.7 306 20 T. maritima GDH 1KQ3-A 29.5 2.6 301 26 E. coli Lactaldehyde reductase 1RRM-A 27.2 3.1 301 16 Ralstonia eutropha Fe-ADH 3JZD-A 26.9 2.9 302 15 Rhizobium sp. MTP-10005 MR 3W5S-A 26.8 3.2 300 15 Klebsiella pneumoniae POR 3BFJ-A 26.7 3.1 302 18 Agrobacterium tumefaciens MR 3HL0-A 26.8 3.0 302 15 Zymomonas mobilis ADH 2 3OWO-A 26.4 3.2 302 16 O. oeni POR 4FR2-A 26.4 3.2 302 20 Corynebacterium glutamicum ADH IV 3IV7-A 26.0 3.1 303 16 T. maritima Butanol dehydrogenase 1VLJ-B 25.2 3.5 299 18 T. maritima Fe-ADH 1VHD-A 25.1 3.2 294 18 Geobacillus thermoglucosidasius ADH 3ZDR-A 24.2 3.2 299 16 Shewanella denitrificans Fe-ADH 3RF7-A 24.2 3.4 290 17 E. coli Hypothetical oxidoreductase YqhD 1OJ7-A 23.6 3.9 300 17 Actinidia chinensis DHQS 3ZOK-D 23.0 3.5 294 16 Mycobacterium tuberculosis DHQS 3QBE-A 22.9 2.9 287 14 Aspergillus nidulans DHQS 1NVB-B 22.3 3.3 290 17 Streptomyces hygroscopicus Cyclase 4P53-A 21.0 2.9 277 16 Staphylococcus aureus DHQS 1XAG-A 20.9 3.3 282 17 Bacillus circulans 2-Deoxy- scyllo -inosose synthase 2GRU-A 20.3 3.2 283 18 Staphylococcus aureus DHQS 1XAH-A 19.5 3.2 264 16 Vibrio cholerae DHQS 3OKF-A 19.4 3.4 280 18 T. thermophilus DHQS 1UJN-A 18.8 3.4 271 14 Helicobacter pylori DHQS 3CLH-A 17.6 3.4 255 21 Open in a separate window a A measure of the statistical significance of the result relative to an alignment of random structures. b Root mean square deviation of α-carbon atoms. c Number of aligned residues. d Sequence identity between the two chains.

Techniques: Binding Assay

Journal: The Journal of Biological Chemistry

Article Title: Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn -Glycerol-1-phosphate Dehydrogenase *

doi: 10.1074/jbc.M115.647461

Figure Lengend Snippet: Top structural alignment hits from the Dali-based structural alignment of MJ G1PDH ( 36 ) MR, maleylacetate reductase; POR, 1,3-propanediol oxidoreductase.

Article Snippet: Previous biochemical characterizations of archaeal G1PDHs have shown the enzyme to be multimeric ( 17 , 42 ). table ft1 table-wrap mode="anchored" t5 TABLE 3 caption a7 Organism Class Protein Data Bank code-monomer Z-score a r.m.s.d. b lali c %id d C. acetobutylicum ATCC 824 GDH 3CE9-A 39.1 2.0 310 34 Sinorhizobium meliloti GDH 3UHJ-A 31.7 2.6 305 21 Geobacillus stearothermophilus GDH 1JQ5-A 30.3 2.5 300 21 Serratia plymuthica A30 GDH 4MCA-A 30.1 2.7 302 21 Schizosaccharomyces pombe GDH 1TA9-B 29.7 2.7 306 20 T. maritima GDH 1KQ3-A 29.5 2.6 301 26 E. coli Lactaldehyde reductase 1RRM-A 27.2 3.1 301 16 Ralstonia eutropha Fe-ADH 3JZD-A 26.9 2.9 302 15 Rhizobium sp. MTP-10005 MR 3W5S-A 26.8 3.2 300 15 Klebsiella pneumoniae POR 3BFJ-A 26.7 3.1 302 18 Agrobacterium tumefaciens MR 3HL0-A 26.8 3.0 302 15 Zymomonas mobilis ADH 2 3OWO-A 26.4 3.2 302 16 O. oeni POR 4FR2-A 26.4 3.2 302 20 Corynebacterium glutamicum ADH IV 3IV7-A 26.0 3.1 303 16 T. maritima Butanol dehydrogenase 1VLJ-B 25.2 3.5 299 18 T. maritima Fe-ADH 1VHD-A 25.1 3.2 294 18 Geobacillus thermoglucosidasius ADH 3ZDR-A 24.2 3.2 299 16 Shewanella denitrificans Fe-ADH 3RF7-A 24.2 3.4 290 17 E. coli Hypothetical oxidoreductase YqhD 1OJ7-A 23.6 3.9 300 17 Actinidia chinensis DHQS 3ZOK-D 23.0 3.5 294 16 Mycobacterium tuberculosis DHQS 3QBE-A 22.9 2.9 287 14 Aspergillus nidulans DHQS 1NVB-B 22.3 3.3 290 17 Streptomyces hygroscopicus Cyclase 4P53-A 21.0 2.9 277 16 Staphylococcus aureus DHQS 1XAG-A 20.9 3.3 282 17 Bacillus circulans 2-Deoxy- scyllo -inosose synthase 2GRU-A 20.3 3.2 283 18 Staphylococcus aureus DHQS 1XAH-A 19.5 3.2 264 16 Vibrio cholerae DHQS 3OKF-A 19.4 3.4 280 18 T. thermophilus DHQS 1UJN-A 18.8 3.4 271 14 Helicobacter pylori DHQS 3CLH-A 17.6 3.4 255 21 Open in a separate window a A measure of the statistical significance of the result relative to an alignment of random structures. b Root mean square deviation of α-carbon atoms. c Number of aligned residues. d Sequence identity between the two chains.

Techniques:

Journal: The Journal of Biological Chemistry

Article Title: Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn -Glycerol-1-phosphate Dehydrogenase *

doi: 10.1074/jbc.M115.647461

Figure Lengend Snippet: Expanded gap version of Dali-lite pairwise structural alignment of MJ G1PDH (36). Selected members of the larger enzyme superfamily including GDHs (Protein Data Bank codes 3CE9 and 1JQ5), ADHs (Protein Data Bank codes 1RRM, 3JZD, 3BFJ, and 4FR2), and DHQSs (Protein Data Bank codes 3QBE, 1XAG, and 1UJN) were used in the alignment. Secondary structural elements and residue numbering correspond to G1PDH. Residues that coordinate metals are highlighted in blue. The coenzyme binding motif is in italics, whereas residues that interact with coenzyme (NADP(H)) and substrate (DHAP) with respect to MJ G1PDH are highlighted in yellow and green, respectively. Reported intersubunit contacts between monomers are in red. Uppercase lettering indicates structurally equivalent positions with G1PDH, whereas lowercase indicates insertions relative to G1PDH.

Article Snippet: Previous biochemical characterizations of archaeal G1PDHs have shown the enzyme to be multimeric ( 17 , 42 ). table ft1 table-wrap mode="anchored" t5 TABLE 3 caption a7 Organism Class Protein Data Bank code-monomer Z-score a r.m.s.d. b lali c %id d C. acetobutylicum ATCC 824 GDH 3CE9-A 39.1 2.0 310 34 Sinorhizobium meliloti GDH 3UHJ-A 31.7 2.6 305 21 Geobacillus stearothermophilus GDH 1JQ5-A 30.3 2.5 300 21 Serratia plymuthica A30 GDH 4MCA-A 30.1 2.7 302 21 Schizosaccharomyces pombe GDH 1TA9-B 29.7 2.7 306 20 T. maritima GDH 1KQ3-A 29.5 2.6 301 26 E. coli Lactaldehyde reductase 1RRM-A 27.2 3.1 301 16 Ralstonia eutropha Fe-ADH 3JZD-A 26.9 2.9 302 15 Rhizobium sp. MTP-10005 MR 3W5S-A 26.8 3.2 300 15 Klebsiella pneumoniae POR 3BFJ-A 26.7 3.1 302 18 Agrobacterium tumefaciens MR 3HL0-A 26.8 3.0 302 15 Zymomonas mobilis ADH 2 3OWO-A 26.4 3.2 302 16 O. oeni POR 4FR2-A 26.4 3.2 302 20 Corynebacterium glutamicum ADH IV 3IV7-A 26.0 3.1 303 16 T. maritima Butanol dehydrogenase 1VLJ-B 25.2 3.5 299 18 T. maritima Fe-ADH 1VHD-A 25.1 3.2 294 18 Geobacillus thermoglucosidasius ADH 3ZDR-A 24.2 3.2 299 16 Shewanella denitrificans Fe-ADH 3RF7-A 24.2 3.4 290 17 E. coli Hypothetical oxidoreductase YqhD 1OJ7-A 23.6 3.9 300 17 Actinidia chinensis DHQS 3ZOK-D 23.0 3.5 294 16 Mycobacterium tuberculosis DHQS 3QBE-A 22.9 2.9 287 14 Aspergillus nidulans DHQS 1NVB-B 22.3 3.3 290 17 Streptomyces hygroscopicus Cyclase 4P53-A 21.0 2.9 277 16 Staphylococcus aureus DHQS 1XAG-A 20.9 3.3 282 17 Bacillus circulans 2-Deoxy- scyllo -inosose synthase 2GRU-A 20.3 3.2 283 18 Staphylococcus aureus DHQS 1XAH-A 19.5 3.2 264 16 Vibrio cholerae DHQS 3OKF-A 19.4 3.4 280 18 T. thermophilus DHQS 1UJN-A 18.8 3.4 271 14 Helicobacter pylori DHQS 3CLH-A 17.6 3.4 255 21 Open in a separate window a A measure of the statistical significance of the result relative to an alignment of random structures. b Root mean square deviation of α-carbon atoms. c Number of aligned residues. d Sequence identity between the two chains.

Techniques: Binding Assay

Journal: The Journal of Biological Chemistry

Article Title: Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn -Glycerol-1-phosphate Dehydrogenase *

doi: 10.1074/jbc.M115.647461

Figure Lengend Snippet: Top structural alignment hits from the Dali-based structural alignment of MJ G1PDH ( 36 ) MR, maleylacetate reductase; POR, 1,3-propanediol oxidoreductase.

Article Snippet: Previous biochemical characterizations of archaeal G1PDHs have shown the enzyme to be multimeric ( 17 , 42 ). table ft1 table-wrap mode="anchored" t5 TABLE 3 caption a7 Organism Class Protein Data Bank code-monomer Z-score a r.m.s.d. b lali c %id d C. acetobutylicum ATCC 824 GDH 3CE9-A 39.1 2.0 310 34 Sinorhizobium meliloti GDH 3UHJ-A 31.7 2.6 305 21 Geobacillus stearothermophilus GDH 1JQ5-A 30.3 2.5 300 21 Serratia plymuthica A30 GDH 4MCA-A 30.1 2.7 302 21 Schizosaccharomyces pombe GDH 1TA9-B 29.7 2.7 306 20 T. maritima GDH 1KQ3-A 29.5 2.6 301 26 E. coli Lactaldehyde reductase 1RRM-A 27.2 3.1 301 16 Ralstonia eutropha Fe-ADH 3JZD-A 26.9 2.9 302 15 Rhizobium sp. MTP-10005 MR 3W5S-A 26.8 3.2 300 15 Klebsiella pneumoniae POR 3BFJ-A 26.7 3.1 302 18 Agrobacterium tumefaciens MR 3HL0-A 26.8 3.0 302 15 Zymomonas mobilis ADH 2 3OWO-A 26.4 3.2 302 16 O. oeni POR 4FR2-A 26.4 3.2 302 20 Corynebacterium glutamicum ADH IV 3IV7-A 26.0 3.1 303 16 T. maritima Butanol dehydrogenase 1VLJ-B 25.2 3.5 299 18 T. maritima Fe-ADH 1VHD-A 25.1 3.2 294 18 Geobacillus thermoglucosidasius ADH 3ZDR-A 24.2 3.2 299 16 Shewanella denitrificans Fe-ADH 3RF7-A 24.2 3.4 290 17 E. coli Hypothetical oxidoreductase YqhD 1OJ7-A 23.6 3.9 300 17 Actinidia chinensis DHQS 3ZOK-D 23.0 3.5 294 16 Mycobacterium tuberculosis DHQS 3QBE-A 22.9 2.9 287 14 Aspergillus nidulans DHQS 1NVB-B 22.3 3.3 290 17 Streptomyces hygroscopicus Cyclase 4P53-A 21.0 2.9 277 16 Staphylococcus aureus DHQS 1XAG-A 20.9 3.3 282 17 Bacillus circulans 2-Deoxy- scyllo -inosose synthase 2GRU-A 20.3 3.2 283 18 Staphylococcus aureus DHQS 1XAH-A 19.5 3.2 264 16 Vibrio cholerae DHQS 3OKF-A 19.4 3.4 280 18 T. thermophilus DHQS 1UJN-A 18.8 3.4 271 14 Helicobacter pylori DHQS 3CLH-A 17.6 3.4 255 21 Open in a separate window a A measure of the statistical significance of the result relative to an alignment of random structures. b Root mean square deviation of α-carbon atoms. c Number of aligned residues. d Sequence identity between the two chains.

Techniques:

Journal:

Article Title: Lessons Drawn from Recent HIV Vaccine Efficacy Trials

doi: 10.1097/QAI.0b013e3181fbca02

Figure Lengend Snippet: HIV Vaccine Efficacy Trials

Article Snippet: We have previously outlined several lessons gleaned from the VAX 004 study, conducted largely among US men who have sex with men (MSM), 4 here we will focus attention on more recent efficacy trials. table ft1 table-wrap mode="anchored" t5 caption a7 Vaccine Strategy Vaccine Manufacturer(s) and Regimen * † Trial (Dates Conducted) Populations and Locations Tested Seroincidence (No. per 100 PY) † ‡ Results Summary Completed Trials Recombinant, monomeric gp120 subunit (B/B; B/E) VaxGen, Inc IM injections at 0,1,6,12,18,24, and 30 mo VAX 004 (1997 2002) VAX 004: 5417 MSM and heterosexual women in the US, Canada, Netherlands Men: 2.7 Women 0.8 Neither VAX 004 or VAX 003 demonstrated efficacy to prevent infection or alter viral load/CD4 count in infected vaccinees 36 , 37 VAX 003 (1999 2003) VAX 003: 2546 male and female Thai IDU Overall: 3.4 Recombinant Ad 5 (clade B gag/pol/nef) Merck, Inc. IM injections at 0, 1, and 6 mo Step (Merck 023/HVTN 502; 2004–2009) (Phambili HVTN 503;2006 2009) 3000 MSM, heterosexual men and women in the US, Canada, Caribbean, South America, Australia 801 South African heterosexual men and women Men V: 3.8; P: 2.8 Women V: 0.52; P: 0.51 Men V:4.2; P: 3.7 Women V:6.8;P: 5.9 No effect on HIV acquisition or early VL set point in Step or Phambili; possible increased HIV infection rate among subgroup of Ad5 seropositive, uncircumcised men in Step 5 ; NS reduction in early VL set point among women in Phambili 12 Recombinant Canarypox virus (ALVAC vcp 1521) prime + monomeric gp120 (B/E) boost Sanofi Aventis (ALVAC) and VaxGen, Inc. IM injections of ALVAC at 0, 1, 3, and 6 mo; gp120 boost at 3 and 6 mo RV144 (2003 2009) 16,402 Thai men and women, largely at heterosexual risk; mostly at low or medium risk of infection Men V: 0.20; P: 0.27 Women V: 0.19; P: 0.31 Modest efficacy to prevent infection in primary MITT 31% (CI 1.1-51%, p=0.04).

Techniques: Recombinant, Infection, Virus