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Isolated rat livers were perfused for 90 min. with oxygenated KRB at 37 C, oxygenated KRB at 43 C, or inadequately oxygenated KRB, containing low glucose, at 43 C. Bile production and GPT, GOT, and K(+) released into the perfusate were measured at zero time and every 15 min. All livers (8 per group) were processed for light and electron microscopy at the end of the 90 min. period. Control livers (37 C) were normal in all aspects monitored. heat alone inhibited bile production after 45 min. and induced elevations in GPT, GOT and K(+) which reached peak levels in 60 min. Light and electron microscopic structure revealed focal hepatocellular damage and generalized endothelial damage. The addition of hypoxia and hypoglycemia to 43 C heat exposure inhibited bile production after 30 min. GPT, GOT, and K(+) release reached peak levels after 45 min. Structural changes were similar to those produced by heat alone except severe damage was uniformly distributed throughout the livers. (Author)

General Biology Lecture

This article is from The Journal of Biological Chemistry , volume 288 . Abstract Background: MurE controls stereochemical incorporation of lysine or diaminopimelate into peptidoglycan stem peptides.Results: The structure of S. aureus MurE reveals an unexpected lack of specificity for lysine within the active site.Conclusion: Incorporation of lysine is supported by the comparatively high concentration of cytoplasmic lysine, not enzyme specificity.Significance: This study provides new perspectives in targeting Gram-positive peptidoglycan assembly for antimicrobial discovery.

This article is from The Journal of Biological Chemistry , volume 288 . Abstract Background: MurE controls stereochemical incorporation of lysine or diaminopimelate into peptidoglycan stem peptides.Results: The structure of S. aureus MurE reveals an unexpected lack of specificity for lysine within the active site.Conclusion: Incorporation of lysine is supported by the comparatively high concentration of cytoplasmic lysine, not enzyme specificity.Significance: This study provides new perspectives in targeting Gram-positive peptidoglycan assembly for antimicrobial discovery.

This article is from BMJ Open , volume 2 . Abstract Objective: Fabry disease (FD) is an X-linked inborn error of glycosphingolipid catabolism caused by deficient lysosomal α-galactosidase A activity. Progressive accumulation of globotriaosylceramide and related glycosphingolipids in vascular endothelial lysosomes of the heart, kidneys and brain is responsible for the main disease manifestations. The aim of our study was to assess short-term and long-term effects of enzyme replacement therapy (ERT) on cardiac mass and function. Design: Retrospective cohort study. Setting: Hospital outpatient clinic. Participants: 40 FD patients (21 men, 19 women) receiving agalsidase β-ERT. Outcome measures: The focus at baseline and follow-up examinations was on structural, functional (Doppler-echocardiography) as well as electrical changes (ECG) and blood pressure. Results: In the Early Group, systolic and diastolic blood pressures significantly decreased. Left-ventricular (LV) also decreased; however, wall thickness and LV mass index showed no further increase. VE as an indicator for diastolic function significantly improved (64±21 vs 75±27 cm/s, p=0.038). There were no significant changes of ECG parameters. There were few relevant changes in the Late Group, albeit systolic blood pressure significantly decreased and QRS duration significantly increased. In conclusion, echocardiographic left-ventricular mass index, interventricular septum thickness, left-ventricular posterior wall, left-ventricular end-diastolic dimension) and diastolic function parameters are valuable for follow-up and guidance of therapy. Conclusions: The primary positive impact of ERT appears to be an early effect after the start of therapy, and early initiation of ERT should be recommended.

This article is from BMC Structural Biology , volume 13 . Abstract Background: In the anaerobic pathway of cobalamin (vitamin B12) synthesis, the CbiT enzyme plays two roles, as a cobalt-precorrin-7 C15-methyltransferase and a C12-decarboxylase, to produce the intermediate, cobalt-precorrin 8. Results: The primary structure of the hypothetical protein MJ0391, from Methanocaldococcus jannaschii, suggested that MJ0391 is a putative CbiT. Here, we report the crystal structure of MJ0391, solved by the MAD procedure and refined to final R-factor and R-free values of 19.8 & 27.3%, respectively, at 2.3 Å resolution. The asymmetric unit contains two NCS molecules, and the intact tetramer generated by crystallographic symmetry may be functionally important. The overall tertiary structure and the tetrameric arrangements are highly homologous to those found in MT0146/CbiT from Methanobacterium thermoautotrophicum. Conclusions: The conservation of functional residues in the binding site for the co-factor, AdoMet, and in the putative precorrin-7 binding pocket suggested that MJ0391 may also possess CbiT activity. The putative function of MJ0391 is discussed, based on structural homology.

Organophosphates (OPs) are a group of pesticides that inhibit enzymes such as acetylcholinesterase. Numerous OP structural variants exist and toxicity data can be difficult to quickly obtain. To address this concern, quantitative structure-activity relationship (QSAR) models were developed to predict acetylcholinesterase, butyrycholinesterase, trypsin and chymotrypsin inhibition, key components in biologically-based dose-response (BBDR) models. The acetylcholinesterase database consisted of 747 structures developed from 69 peer reviewed publications. AMPAC and CODESSA descriptors (SemiChem, Inc.) were calculated for each compound. The acetylcholinesterase results show that the average nucleophilic reactive index for a carbon atom contributed most significantly to binding. A training R2 of 0.73-0.01 and an external test set Q2 of 0.62-0.06 was achieved. The QSAR models discussed in this seminar will complement OP BBDR modeling by filling critical data gaps for key parameter values, leading to better risk assessment and prioritization of animal and human toxicity studies especially for OPs lacking experimental data.

This article is from PLoS ONE , volume 9 . Abstract Organochlorine insecticide hexachlorocyclohexane (HCH) has recently been classified as a ‘Persistent Organic pollutant’ by the Stockholm Convention. The LinB haloalkane dehalogenase is a key upstream enzyme in the recently evolved Lin pathway for the catabolism of HCH in bacteria. Here we report a sequence-structure-function analysis of ten naturally occurring and thirteen synthetic mutants of LinB. One of the synthetic mutants was found to have ∼80 fold more activity for β- and δ-hexachlorocyclohexane. Based on detailed biophysical calculations, molecular dynamics and ensemble docking calculations, we propose that the latter variant is more active because of alterations to the shape of its active site and increased conformational plasticity.

This article is from PLoS ONE , volume 9 . Abstract Organochlorine insecticide hexachlorocyclohexane (HCH) has recently been classified as a ‘Persistent Organic pollutant’ by the Stockholm Convention. The LinB haloalkane dehalogenase is a key upstream enzyme in the recently evolved Lin pathway for the catabolism of HCH in bacteria. Here we report a sequence-structure-function analysis of ten naturally occurring and thirteen synthetic mutants of LinB. One of the synthetic mutants was found to have ∼80 fold more activity for β- and δ-hexachlorocyclohexane. Based on detailed biophysical calculations, molecular dynamics and ensemble docking calculations, we propose that the latter variant is more active because of alterations to the shape of its active site and increased conformational plasticity.

This article is from Molecular Microbiology , volume 91 . Abstract Bis‐(3′,5′) cyclic di‐guanylate (c‐di‐GMP) is a key bacterial second messenger that is implicated in the regulation of many crucial processes that include biofilm formation, motility and virulence. Cellular levels of c‐di‐GMP are controlled through synthesis by GGDEF domain diguanylate cyclases and degradation by two classes of phosphodiesterase with EAL or HD‐GYP domains. Here, we have determined the structure of an enzymatically active HD‐GYP domain protein from Persephonella marina (PmGH) alone, in complex with substrate (c‐di‐GMP) and final reaction product (GMP). The structures reveal a novel trinuclear iron binding site, which is implicated in catalysis and identify residues involved in recognition of c‐di‐GMP. This structure completes the picture of all domains involved in c‐di‐GMP metabolism and reveals that the HD‐GYP family splits into two distinct subgroups containing bi‐ and trinuclear metal centres.

This article is from Molecular Microbiology , volume 91 . Abstract Bis‐(3′,5′) cyclic di‐guanylate (c‐di‐GMP) is a key bacterial second messenger that is implicated in the regulation of many crucial processes that include biofilm formation, motility and virulence. Cellular levels of c‐di‐GMP are controlled through synthesis by GGDEF domain diguanylate cyclases and degradation by two classes of phosphodiesterase with EAL or HD‐GYP domains. Here, we have determined the structure of an enzymatically active HD‐GYP domain protein from Persephonella marina (PmGH) alone, in complex with substrate (c‐di‐GMP) and final reaction product (GMP). The structures reveal a novel trinuclear iron binding site, which is implicated in catalysis and identify residues involved in recognition of c‐di‐GMP. This structure completes the picture of all domains involved in c‐di‐GMP metabolism and reveals that the HD‐GYP family splits into two distinct subgroups containing bi‐ and trinuclear metal centres.

This article is from Molecular Microbiology , volume 91 . Abstract Bis‐(3′,5′) cyclic di‐guanylate (c‐di‐GMP) is a key bacterial second messenger that is implicated in the regulation of many crucial processes that include biofilm formation, motility and virulence. Cellular levels of c‐di‐GMP are controlled through synthesis by GGDEF domain diguanylate cyclases and degradation by two classes of phosphodiesterase with EAL or HD‐GYP domains. Here, we have determined the structure of an enzymatically active HD‐GYP domain protein from Persephonella marina (PmGH) alone, in complex with substrate (c‐di‐GMP) and final reaction product (GMP). The structures reveal a novel trinuclear iron binding site, which is implicated in catalysis and identify residues involved in recognition of c‐di‐GMP. This structure completes the picture of all domains involved in c‐di‐GMP metabolism and reveals that the HD‐GYP family splits into two distinct subgroups containing bi‐ and trinuclear metal centres.

General Biology Lecture

General Biology Lecture

This article is from Biotechnology for Biofuels , volume 5 . Abstract Background: Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars.However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. Results: In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. Conclusion: The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.

This article is from Molecular Microbiology , volume 93 . Abstract Some bacteria and archaea synthesize haem by an alternative pathway, which involves the sequestration of sirohaem as a metabolic intermediate rather than as a prosthetic group. Along this pathway the two acetic acid side-chains attached to C12 and C18 are decarboxylated by sirohaem decarboxylase, a heterodimeric enzyme composed of AhbA and AhbB, to give didecarboxysirohaem. Further modifications catalysed by two related radical SAM enzymes, AhbC and AhbD, transform didecarboxysirohaem into Fe-coproporphyrin III and haem respectively. The characterization of sirohaem decarboxylase is reported in molecular detail. Recombinant versions of Desulfovibrio desulfuricans, Desulfovibrio vulgaris and Methanosarcina barkeri AhbA/B have been produced and their physical properties compared. The D. vulgaris and M. barkeri enzyme complexes both copurify with haem, whose redox state influences the activity of the latter. The kinetic parameters of the D. desulfuricans enzyme have been determined, the enzyme crystallized and its structure has been elucidated. The topology of the enzyme reveals that it shares a structural similarity to the AsnC/Lrp family of transcription factors. The active site is formed in the cavity between the two subunits and a AhbA/B-product complex with didecarboxysirohaem has been obtained. A mechanism for the decarboxylation of the kinetically stable carboxyl groups is proposed.

This article is from International Journal of Molecular Sciences , volume 13 . Abstract The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms. Ionic radiation and sunlight are known producers of Reactive Oxygen Species (ROS), one of the causes for DNA lesions. The damaged DNA is repaired by many enzymes, among of them Base Excision Repair enzymes, producing the highly mutagenic apurinic/apyrimidinicsites (AP sites). Therefore, recognition of AP sites is fundamental to cell/organism survival. In the present work, the full coding sequence of a putative cAPEX1 gene was amplified for the first time from C. dromedarius by RT-PCR and cloned (NCBI accession number are HM209828 and ADJ96599 for nucleotides and amino acids, respectively). cDNA sequencing was deduced to be 1041 nucleotides, of which 954 nucleotides encode a protein of 318 amino acids, similar to the coding region of the APEX1 gene and the protein from many other species. The calculated molecular weight and isoelectric point of cAPEX1 using Bioinformatics tools was 35.5 kDa and 8.11, respectively. The relative expressions of cAPEX1 in camel kidney, spleen, lung and testis were examined using qPCR and compared with that of the liver using a 18S ribosomal subunit as endogenous control. The highest level of cAPEX1 transcript was found in the testis; 325% higher than the liver, followed by spleen (87%), kidney (20%) and lung (5%), respectively. The cAPEX1 is 94%–97% similar to their mammalian counterparts. Phylogenetic analysis revealed that cAPEX1 is grouped together with that of S. scrofa. The predicted 3D structure of cAPEX1 has similar folds and topology with the human (hAPEX1). The root-mean-square deviation (rmsd) between cAPEX1 and hAPEX1 was 0.582 and the Q-score was 0.939.

This article is from International Journal of Molecular Sciences , volume 13 . Abstract The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms. Ionic radiation and sunlight are known producers of Reactive Oxygen Species (ROS), one of the causes for DNA lesions. The damaged DNA is repaired by many enzymes, among of them Base Excision Repair enzymes, producing the highly mutagenic apurinic/apyrimidinicsites (AP sites). Therefore, recognition of AP sites is fundamental to cell/organism survival. In the present work, the full coding sequence of a putative cAPEX1 gene was amplified for the first time from C. dromedarius by RT-PCR and cloned (NCBI accession number are HM209828 and ADJ96599 for nucleotides and amino acids, respectively). cDNA sequencing was deduced to be 1041 nucleotides, of which 954 nucleotides encode a protein of 318 amino acids, similar to the coding region of the APEX1 gene and the protein from many other species. The calculated molecular weight and isoelectric point of cAPEX1 using Bioinformatics tools was 35.5 kDa and 8.11, respectively. The relative expressions of cAPEX1 in camel kidney, spleen, lung and testis were examined using qPCR and compared with that of the liver using a 18S ribosomal subunit as endogenous control. The highest level of cAPEX1 transcript was found in the testis; 325% higher than the liver, followed by spleen (87%), kidney (20%) and lung (5%), respectively. The cAPEX1 is 94%–97% similar to their mammalian counterparts. Phylogenetic analysis revealed that cAPEX1 is grouped together with that of S. scrofa. The predicted 3D structure of cAPEX1 has similar folds and topology with the human (hAPEX1). The root-mean-square deviation (rmsd) between cAPEX1 and hAPEX1 was 0.582 and the Q-score was 0.939.

This article is from International Journal of Molecular Sciences , volume 13 . Abstract The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms. Ionic radiation and sunlight are known producers of Reactive Oxygen Species (ROS), one of the causes for DNA lesions. The damaged DNA is repaired by many enzymes, among of them Base Excision Repair enzymes, producing the highly mutagenic apurinic/apyrimidinicsites (AP sites). Therefore, recognition of AP sites is fundamental to cell/organism survival. In the present work, the full coding sequence of a putative cAPEX1 gene was amplified for the first time from C. dromedarius by RT-PCR and cloned (NCBI accession number are HM209828 and ADJ96599 for nucleotides and amino acids, respectively). cDNA sequencing was deduced to be 1041 nucleotides, of which 954 nucleotides encode a protein of 318 amino acids, similar to the coding region of the APEX1 gene and the protein from many other species. The calculated molecular weight and isoelectric point of cAPEX1 using Bioinformatics tools was 35.5 kDa and 8.11, respectively. The relative expressions of cAPEX1 in camel kidney, spleen, lung and testis were examined using qPCR and compared with that of the liver using a 18S ribosomal subunit as endogenous control. The highest level of cAPEX1 transcript was found in the testis; 325% higher than the liver, followed by spleen (87%), kidney (20%) and lung (5%), respectively. The cAPEX1 is 94%–97% similar to their mammalian counterparts. Phylogenetic analysis revealed that cAPEX1 is grouped together with that of S. scrofa. The predicted 3D structure of cAPEX1 has similar folds and topology with the human (hAPEX1). The root-mean-square deviation (rmsd) between cAPEX1 and hAPEX1 was 0.582 and the Q-score was 0.939.

This article is from International Journal of Molecular Sciences , volume 13 . Abstract The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms. Ionic radiation and sunlight are known producers of Reactive Oxygen Species (ROS), one of the causes for DNA lesions. The damaged DNA is repaired by many enzymes, among of them Base Excision Repair enzymes, producing the highly mutagenic apurinic/apyrimidinicsites (AP sites). Therefore, recognition of AP sites is fundamental to cell/organism survival. In the present work, the full coding sequence of a putative cAPEX1 gene was amplified for the first time from C. dromedarius by RT-PCR and cloned (NCBI accession number are HM209828 and ADJ96599 for nucleotides and amino acids, respectively). cDNA sequencing was deduced to be 1041 nucleotides, of which 954 nucleotides encode a protein of 318 amino acids, similar to the coding region of the APEX1 gene and the protein from many other species. The calculated molecular weight and isoelectric point of cAPEX1 using Bioinformatics tools was 35.5 kDa and 8.11, respectively. The relative expressions of cAPEX1 in camel kidney, spleen, lung and testis were examined using qPCR and compared with that of the liver using a 18S ribosomal subunit as endogenous control. The highest level of cAPEX1 transcript was found in the testis; 325% higher than the liver, followed by spleen (87%), kidney (20%) and lung (5%), respectively. The cAPEX1 is 94%–97% similar to their mammalian counterparts. Phylogenetic analysis revealed that cAPEX1 is grouped together with that of S. scrofa. The predicted 3D structure of cAPEX1 has similar folds and topology with the human (hAPEX1). The root-mean-square deviation (rmsd) between cAPEX1 and hAPEX1 was 0.582 and the Q-score was 0.939.

This article is from International Journal of Molecular Sciences , volume 13 . Abstract The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms. Ionic radiation and sunlight are known producers of Reactive Oxygen Species (ROS), one of the causes for DNA lesions. The damaged DNA is repaired by many enzymes, among of them Base Excision Repair enzymes, producing the highly mutagenic apurinic/apyrimidinicsites (AP sites). Therefore, recognition of AP sites is fundamental to cell/organism survival. In the present work, the full coding sequence of a putative cAPEX1 gene was amplified for the first time from C. dromedarius by RT-PCR and cloned (NCBI accession number are HM209828 and ADJ96599 for nucleotides and amino acids, respectively). cDNA sequencing was deduced to be 1041 nucleotides, of which 954 nucleotides encode a protein of 318 amino acids, similar to the coding region of the APEX1 gene and the protein from many other species. The calculated molecular weight and isoelectric point of cAPEX1 using Bioinformatics tools was 35.5 kDa and 8.11, respectively. The relative expressions of cAPEX1 in camel kidney, spleen, lung and testis were examined using qPCR and compared with that of the liver using a 18S ribosomal subunit as endogenous control. The highest level of cAPEX1 transcript was found in the testis; 325% higher than the liver, followed by spleen (87%), kidney (20%) and lung (5%), respectively. The cAPEX1 is 94%–97% similar to their mammalian counterparts. Phylogenetic analysis revealed that cAPEX1 is grouped together with that of S. scrofa. The predicted 3D structure of cAPEX1 has similar folds and topology with the human (hAPEX1). The root-mean-square deviation (rmsd) between cAPEX1 and hAPEX1 was 0.582 and the Q-score was 0.939.

This article is from Nucleic Acids Research , volume 42 . Abstract AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves deoxyribonucleic acid (DNA) containing 5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA containing unmodified cytosine. AbaSI has been used as a tool for mapping the genomic locations of 5hmC, an important epigenetic modification in the DNA of higher organisms. Here we report the crystal structures of AbaSI in the presence and absence of DNA. These structures provide considerable, although incomplete, insight into how this enzyme acts. AbaSI appears to be mainly a homodimer in solution, but interacts with DNA in our structures as a homotetramer. Each AbaSI subunit comprises an N-terminal, Vsr-like, cleavage domain containing a single catalytic site, and a C-terminal, SRA-like, 5hmC-binding domain. Two N-terminal helices mediate most of the homodimer interface. Dimerization brings together the two catalytic sites required for double-strand cleavage, and separates the 5hmC binding-domains by ∼70 Å, consistent with the known activity of AbaSI which cleaves DNA optimally between symmetrically modified cytosines ∼22 bp apart. The eukaryotic SET and RING-associated (SRA) domains bind to DNA containing 5-methylcytosine (5mC) in the hemi-methylated CpG sequence. They make contacts in both the major and minor DNA grooves, and flip the modified cytosine out of the helix into a conserved binding pocket. In contrast, the SRA-like domain of AbaSI, which has no sequence specificity, contacts only the minor DNA groove, and in our current structures the 5hmC remains intra-helical. A conserved, binding pocket is nevertheless present in this domain, suitable for accommodating 5hmC and g5hmC. We consider it likely, therefore, that base-flipping is part of the recognition and cleavage mechanism of AbaSI, but that our structures represent an earlier, pre-flipped stage, prior to actual recognition.

This article is from Nucleic Acids Research , volume 42 . Abstract AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves deoxyribonucleic acid (DNA) containing 5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA containing unmodified cytosine. AbaSI has been used as a tool for mapping the genomic locations of 5hmC, an important epigenetic modification in the DNA of higher organisms. Here we report the crystal structures of AbaSI in the presence and absence of DNA. These structures provide considerable, although incomplete, insight into how this enzyme acts. AbaSI appears to be mainly a homodimer in solution, but interacts with DNA in our structures as a homotetramer. Each AbaSI subunit comprises an N-terminal, Vsr-like, cleavage domain containing a single catalytic site, and a C-terminal, SRA-like, 5hmC-binding domain. Two N-terminal helices mediate most of the homodimer interface. Dimerization brings together the two catalytic sites required for double-strand cleavage, and separates the 5hmC binding-domains by ∼70 Å, consistent with the known activity of AbaSI which cleaves DNA optimally between symmetrically modified cytosines ∼22 bp apart. The eukaryotic SET and RING-associated (SRA) domains bind to DNA containing 5-methylcytosine (5mC) in the hemi-methylated CpG sequence. They make contacts in both the major and minor DNA grooves, and flip the modified cytosine out of the helix into a conserved binding pocket. In contrast, the SRA-like domain of AbaSI, which has no sequence specificity, contacts only the minor DNA groove, and in our current structures the 5hmC remains intra-helical. A conserved, binding pocket is nevertheless present in this domain, suitable for accommodating 5hmC and g5hmC. We consider it likely, therefore, that base-flipping is part of the recognition and cleavage mechanism of AbaSI, but that our structures represent an earlier, pre-flipped stage, prior to actual recognition.

General Biology Lecture

General Biology Lecture

This article is from Biochemical Journal , volume 452 . Abstract The competition between viruses and hosts is played out in all branches of life. Many prokaryotes have an adaptive immune system termed ‘CRISPR’ (clustered regularly interspaced short palindromic repeats) which is based on the capture of short pieces of viral DNA. The captured DNA is integrated into the genomic DNA of the organism flanked by direct repeats, transcribed and processed to generate crRNA (CRISPR RNA) that is loaded into a variety of effector complexes. These complexes carry out sequence-specific detection and destruction of invading mobile genetic elements. In the present paper, we report the structure and activity of a Cas6 (CRISPR-associated 6) enzyme (Sso1437) from Sulfolobus solfataricus responsible for the generation of unit-length crRNA species. The crystal structure reveals an unusual dimeric organization that is important for the enzyme's activity. In addition, the active site lacks the canonical catalytic histidine residue that has been viewed as an essential feature of the Cas6 family. Although several residues contribute towards catalysis, none is absolutely essential. Coupled with the very low catalytic rate constants of the Cas6 family and the plasticity of the active site, this suggests that the crRNA recognition and chaperone-like activities of the Cas6 family should be considered as equal to or even more important than their role as traditional enzymes.

This article is from Biochemical Journal , volume 452 . Abstract The competition between viruses and hosts is played out in all branches of life. Many prokaryotes have an adaptive immune system termed ‘CRISPR’ (clustered regularly interspaced short palindromic repeats) which is based on the capture of short pieces of viral DNA. The captured DNA is integrated into the genomic DNA of the organism flanked by direct repeats, transcribed and processed to generate crRNA (CRISPR RNA) that is loaded into a variety of effector complexes. These complexes carry out sequence-specific detection and destruction of invading mobile genetic elements. In the present paper, we report the structure and activity of a Cas6 (CRISPR-associated 6) enzyme (Sso1437) from Sulfolobus solfataricus responsible for the generation of unit-length crRNA species. The crystal structure reveals an unusual dimeric organization that is important for the enzyme's activity. In addition, the active site lacks the canonical catalytic histidine residue that has been viewed as an essential feature of the Cas6 family. Although several residues contribute towards catalysis, none is absolutely essential. Coupled with the very low catalytic rate constants of the Cas6 family and the plasticity of the active site, this suggests that the crRNA recognition and chaperone-like activities of the Cas6 family should be considered as equal to or even more important than their role as traditional enzymes.

This article is from Biochemical Journal , volume 452 . Abstract The competition between viruses and hosts is played out in all branches of life. Many prokaryotes have an adaptive immune system termed ‘CRISPR’ (clustered regularly interspaced short palindromic repeats) which is based on the capture of short pieces of viral DNA. The captured DNA is integrated into the genomic DNA of the organism flanked by direct repeats, transcribed and processed to generate crRNA (CRISPR RNA) that is loaded into a variety of effector complexes. These complexes carry out sequence-specific detection and destruction of invading mobile genetic elements. In the present paper, we report the structure and activity of a Cas6 (CRISPR-associated 6) enzyme (Sso1437) from Sulfolobus solfataricus responsible for the generation of unit-length crRNA species. The crystal structure reveals an unusual dimeric organization that is important for the enzyme's activity. In addition, the active site lacks the canonical catalytic histidine residue that has been viewed as an essential feature of the Cas6 family. Although several residues contribute towards catalysis, none is absolutely essential. Coupled with the very low catalytic rate constants of the Cas6 family and the plasticity of the active site, this suggests that the crRNA recognition and chaperone-like activities of the Cas6 family should be considered as equal to or even more important than their role as traditional enzymes.

This article is from Nucleic Acids Research , volume 42 . Abstract The B3 DNA-binding domains (DBDs) of plant transcription factors (TF) and DBDs of EcoRII and BfiI restriction endonucleases (EcoRII-N and BfiI-C) share a common structural fold, classified as the DNA-binding pseudobarrel. The B3 DBDs in the plant TFs recognize a diverse set of target sequences. The only available co-crystal structure of the B3-like DBD is that of EcoRII-N (recognition sequence 5′-CCTGG-3′). In order to understand the structural and molecular mechanisms of specificity of B3 DBDs, we have solved the crystal structure of BfiI-C (recognition sequence 5′-ACTGGG-3′) complexed with 12-bp cognate oligoduplex. Structural comparison of BfiI-C–DNA and EcoRII-N–DNA complexes reveals a conserved DNA-binding mode and a conserved pattern of interactions with the phosphodiester backbone. The determinants of the target specificity are located in the loops that emanate from the conserved structural core. The BfiI-C–DNA structure presented here expands a range of templates for modeling of the DNA-bound complexes of the B3 family of plant TFs.

Studies on the structural of acetyicholinesterase (AChE) as a target of organophosphate toxicity continue and have yielded several leads of significance and practical outcomes. First, studies on oxime reactivation reveal the importance of achieving a suitable angle of attack for the oxime within the confines of the active center gorge. Through the use of mutant AChE-oxime combinations, oxime assisted catalytic turnover of organophosphates can be achieved such that mutant AChE can be employed with oximes as a catalytic scavenger. Second, through cysteine substitution mutagenesis and acrylodan labeling we have developed a fluorescent enzyme whose emission spectrmn changes upon conjugation with organophosphate. These enzymes are now being immobilized and developed as a remote sensor for acetylcholinesterase. Third, we have developed mass spectrometry methods to detect directly the organophosphate conjugates with AChE. Lastly, we have developed several transgenic animal strains that enable us to study the roles cholinesterase inhibition centrally and in the periphery play in organophosphate toxicity and whether the antidotal actions of oximes arise solely through reactivation.

Studies on the structural of acetyicholinesterase (AChE) as a target of organophosphate toxicity continue and have yielded several leads of significance and practical outcomes. First, studies on oxime reactivation reveal the importance of achieving a suitable angle of attack for the oxime within the confines of the active center gorge. Through the use of mutant AChE-oxime combinations, oxime assisted catalytic turnover of organophosphates can be achieved such that mutant AChE can be employed with oximes as a catalytic scavenger. Second, through cysteine substitution mutagenesis and acrylodan labeling we have developed a fluorescent enzyme whose emission spectrmn changes upon conjugation with organophosphate. These enzymes are now being immobilized and developed as a remote sensor for acetylcholinesterase. Third, we have developed mass spectrometry methods to detect directly the organophosphate conjugates with AChE. Lastly, we have developed several transgenic animal strains that enable us to study the roles cholinesterase inhibition centrally and in the periphery play in organophosphate toxicity and whether the antidotal actions of oximes arise solely through reactivation.

Studies on the structural of acetyicholinesterase (AChE) as a target of organophosphate toxicity continue and have yielded several leads of significance and practical outcomes. First, studies on oxime reactivation reveal the importance of achieving a suitable angle of attack for the oxime within the confines of the active center gorge. Through the use of mutant AChE-oxime combinations, oxime assisted catalytic turnover of organophosphates can be achieved such that mutant AChE can be employed with oximes as a catalytic scavenger. Second, through cysteine substitution mutagenesis and acrylodan labeling we have developed a fluorescent enzyme whose emission spectrmn changes upon conjugation with organophosphate. These enzymes are now being immobilized and developed as a remote sensor for acetylcholinesterase. Third, we have developed mass spectrometry methods to detect directly the organophosphate conjugates with AChE. Lastly, we have developed several transgenic animal strains that enable us to study the roles cholinesterase inhibition centrally and in the periphery play in organophosphate toxicity and whether the antidotal actions of oximes arise solely through reactivation.

This article is from Nanoscale Research Letters , volume 9 . Abstract In this work, a commercial peroxidase was immobilized onto porous silicon (PS) support functionalized with 3-aminopropyldiethoxysilane (APDES) and the performance of the obtained catalytic microreactor was studied. The immobilization steps were monitored and the activity of the immobilized enzyme in the PS pores was spectrophotometrically determined. The enzyme immobilization in porous silicon has demonstrated its potential as highly efficient enzymatic reactor. The effect of a polar organic solvent (acetonitrile) and the temperature (up to 50°C) on the activity and stability of the biocatalytic microreactor were studied. After 2-h incubation in organic solvent, the microreactor retained 80% of its initial activity in contrast to the system with free soluble peroxidase that lost 95% of its activity in the same period of time. Peroxidase immobilized into the spaces of the porous silicon support would be perspective for applications in treatments for environmental security such as removal of leached dye in textile industry or in treatment of different industrial effluents. The system can be also applied in the field of biomedicine.

This article is from BMC Plant Biology , volume 11 . Abstract Background: Two distinct starch branching enzyme (SBE) isoforms predate the divergence of monocots and dicots and have been conserved in plants since then. This strongly suggests that both SBEI and SBEII provide unique selective advantages to plants. However, no phenotype for the SBEI mutation, sbe1a, had been previously observed. To explore this incongruity the objective of the present work was to characterize functional and molecular phenotypes of both sbe1a and wild-type (Wt) in the W64A maize inbred line. Results: Endosperm starch granules from the sbe1a mutant were more resistant to digestion by pancreatic α-amylase, and the sbe1a mutant starch had an altered branching pattern for amylopectin and amylose. When kernels were germinated, the sbe1a mutant was associated with shorter coleoptile length and higher residual starch content, suggesting that less efficient starch utilization may have impaired growth during germination. Conclusions: The present report documents for the first time a molecular phenotype due to the absence of SBEI, and suggests strongly that it is associated with altered physiological function of the starch in vivo. We believe that these results provide a plausible rationale for the conservation of SBEI in plants in both monocots and dicots, as greater seedling vigor would provide an important survival advantage when resources are limited.

Studies on the structure of acetylcholinesterase (AChE) as a target for organophosphate toxicity continue and have resulted in several leads of significance. First, we have completed the first phase of studies of the structural determinants on the enzyme responsible for inactivation and oxime reactivation. The oxime reactivation studies reveal mutations whereby reactivation can be accelerated some 100-fold, and the combination oxime-mutant AChE shows promise as a prophylactic agent or antidote. Second, through cysteine-substitution mutagenesis and labeling, we have developed steady-state and anisotrophy decay fluorescence methods to examine segmental motion in the protein. This has yielded valuable information on the flexibility of the active center gorge, and the practical outcome of a potentially high sensitivity detection method for organophosphate exposure using the enzyme target as a detector. Third, we have developed an analytical means of measuring organophosphate exposure by MALDI-TOF mass spectrometry that actually measures the product rather than drawing inferences from inhibition of activity. Lastly, several other studies related to our overall objectives are underway. The first is the production of gene knockouts for all of the cholinesterase splice variants.

Nucleoside modifications are significant structural components of most classes of cellular Ribonucleic Acids. About 50 RNA modifications are known, varying in complexity from simple base or sugar methylations to multifunctional heterocyclic groups. The use of RNA modification enzymes as probes of protein-nucleic acid interaction has been limited by the lack of pure enzymes of this type. Our goal is to develop the pseudouridine modification system for this purpose, by identifying the enzymes, genes and molecular interactions involved in the synthesis of this nucleoside.

Crystal structure of FadD32, an enzyme essential for mycolic acid biosynthesis in mycobacteria 作者： Li, Wenjuan 1 Gu, Shoujin 1 Fleming, Joy 1 Bi, Lijun 1 Gu, Shoujin 2 作者单位： 1. Chinese Acad Sci, Inst Biophys, Key Lab RNA Biol, Beijing 100080, Peoples R China. 2. Univ Chinese Acad Sci, Beijing, Peoples R China. 提交时间： 2016-05-11 摘要: Fatty acid degradation protein D32 (FadD32), an enzyme required for mycolic acid biosynthesis and essential for mycobacterial growth, has recently been identified as a valid and promising target for anti-tuberculosis drug development. Here we report the crystal structures of Mycobacterium smegmatis FadD32 in the apo and ATP-bound states at 2.4 angstrom and 2.25 angstrom resolution, respectively. FadD32 consists of two globular domains connected by a flexible linker. ATP binds in a cleft at the interface between the N- and C-terminal domains and its binding induces significant local conformational changes in FadD32. The binding sites of meromycolic acid and phosphopantetheine are identified by structural comparison with other members of the adenylating enzyme superfamily. These results will improve our understanding of the catalytic mechanism of FadD32 and help in the design of inhibitors of this essential enzyme. ACYL-AMP LIGASE TUBERCULOSIS ACTIVATION SYNTHETASE BIOGENESIS DOMAINS 期刊： SCIENTIFIC REPORTS 分类： 生物学 >> 生物物理学 引用： ChinaXiv:201605.01287 (或此版本 ChinaXiv:201605.01287V1 ) doi:10.12074/201605.01287 CSTR:32003.36.ChinaXiv.201605.01287.V1 推荐引用方式： Li, Wenjuan,Gu, Shoujin,Fleming, Joy,Bi, Lijun,Gu, Shoujin.(2016).Crystal structure of FadD32, an enzyme essential for mycolic acid biosynthesis in mycobacteria.SCIENTIFIC REPORTS.[ChinaXiv:201605.01287] 版本历史 [V1] 2016-05-11 08:40:37 ChinaXiv:201605.01287V1 下载全文

Studies on the structural of acetylcholinesterase (AChE) as a target of organophosphate toxicity continue and have yielded several leads of significance and practical outcomes. First, studies on oxime reactivation reveal the importance of achieving a suitable angle of attack for the oxime within the confines of the active center gorge. Through the use of mutant AChE-oxime combinations, oxime-assisted catalytic turnover of organophosphates can be achieved such that mutant AChE can be employed with oximes as a catalytic scavenger. Second, through cysteine substitution mutagenesis and acrylodan labeling we have developed a fluorescent enzyme whose emission spectrum changes upon conjugation with organophosphate. These enzymes are now being immobilized and developed as remote sensors for AChE inhibition. Third, we have developed mass spectrometry methods to detect directly the organophosphate conjugates with AChE. Lastly, we have developed several transgenic (knock-out) animal strains that enable us to study the roles cholinesterase inhibition centrally and in the periphery play in organophosphate toxicity and whether the antidotal actions of oximes arise solely through reactivation.