Structural genomics: keeping up with expanding knowledge of the protein universe

Grabowski, M.; Joachimiak, Andrzej; Otwinowski, Zbyszek; Minor, Władek

doi:10.1016/j.sbi.2007.06.003

Cited by 40 publications

(33 citation statements)

References 29 publications

(11 reference statements)

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“…As an area of extensive research in the postgenomic era, structural genomics (also known as structural proteomics) projects are being conducted worldwide and expending great efforts toward expanding knowledge of the protein universe (1)(2)(3). Basically, structural genomics aims to understand the relationship between protein sequence, structure, and function, by determining the structure of uncharacterized gene products (4).…”

Section: Introductionmentioning

confidence: 99%

HP0902 from Helicobacter pylori is a thermostable, dimeric protein belonging to an all-β topology of the cupin superfamily

Sim

Lee²,

Kim³

et al. 2009

BMB Reports

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Section: Introductionmentioning

confidence: 99%

HP0902 from Helicobacter pylori is a thermostable, dimeric protein belonging to an all-β topology of the cupin superfamily

Sim

Lee²,

Kim³

et al. 2009

BMB Reports

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“…Several genome and transcriptome sequencing projects have been carried out around the world leading to a rapid expansion of knowledge of the protein universe (Grabowski et al 2007). In the case of AMP, small size and extreme sequence divergence lead to difficulties in identifying new groups and new families.…”

mentioning

confidence: 99%

Evolutionary relationship between defensins in the Poaceae family strengthened by the characterization of new sugarcane defensins

et al. 2008

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Plant defensins are small (45-54 amino acids), highly basic, cysteine-rich peptides structurally related to defensins of other organisms, including insects and mammals. Small putative proteins (MW < 10 kDa) containing eight cysteines were screened based on the sugarcane expressed sequence tag (EST) database. We selected ORFs that exhibited 25-100% similarity in primary sequence with other defensins in the NCBI database and that contained eight cysteines. This similarity is sufficient for folding prediction, but not enough for biological activity inference. Six putative defensins (Sd1-6) were selected, and activity assays showed that recombinant Sd1, Sd3 and Sd5 are active against fungi, but not against bacteria. Structural characterization, based on circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy showed that the structures of these Sds were compatible with alpha/beta proteins, a feature expected for plant defensins. Phylogenetic analysis revealed that sugarcane defensins could clearly be grouped within defensins from Poaceae family and Andropogoneae tribe. Our work demonstrates that defensins show strong conservation in the Poaceae family and may indicate that the same conservation occurs in other families. We suggest that evolutionary relationships within plant families can be used as a procedure to predict and annotate new defensins in genomes and group them in evolutionary classes to help in the investigation of their biological function.

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“…A brief status report on the "protein universe" effort is provided for context; this field has been reviewed elsewhere (33,(54)(55)(56)(57).…”

Section: The Beginning Of Structural Genomicsmentioning

confidence: 99%

Large-Scale Structural Biology of the Human Proteome

Edwards

2009

Annu. Rev. Biochem.

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The large-scale structural biology projects that target human proteins focus predominantly on the catalytic domains of potential therapeutic targets and the domains of human proteins that mediate protein-protein and protein-small-molecule interactions. Their main scientific objective is to elucidate the molecular basis for specificity and selectivity of function within large protein families of therapeutic interest, such as kinases, phosphatases, and proteins involved in epigenetic regulation. Half of the unique human protein structures determined in the past three years derive from these initiatives.

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Structural genomics: keeping up with expanding knowledge of the protein universe

Cited by 40 publications

References 29 publications

HP0902 from Helicobacter pylori is a thermostable, dimeric protein belonging to an all-β topology of the cupin superfamily

HP0902 from Helicobacter pylori is a thermostable, dimeric protein belonging to an all-β topology of the cupin superfamily

Evolutionary relationship between defensins in the Poaceae family strengthened by the characterization of new sugarcane defensins

Large-Scale Structural Biology of the Human Proteome

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