The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

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Initial sequencing and analysis of the human genome.

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

CHAPTER 24 – Evolution of Protein Molecules

Semiconductor nanocrystals were prepared for use as fluorescent probes in biological staining and diagnostics. Compared with conventional fluorophores, the nanocrystals have a narrow, tunable, symmetric emission spectrum and are photochemically stable. The advantages of the broad, continuous excitation spectrum were demonstrated in a dual-emission, single-excitation labeling experiment on mouse fibroblasts. These nanocrystal probes are thus complementary and in some cases may be superior to existing fluorophores.

https://science.sciencemag.org/content/sci/281/5385/2013.full.pdf

Semiconductor Nanocrystals as Fluorescent Biological Labels

Highly luminescent semiconductor quantum dots (zinc sulfide-capped cadmium selenide) have been covalently coupled to biomolecules for use in ultrasensitive biological detection. In comparison with organic dyes such as rhodamine, this class of luminescent labels is 20 times as bright, 100 times as stable against photobleaching, and one-third as wide in spectral linewidth. These nanometer-sized conjugates are water-soluble and biocompatible. Quantum dots that were labeled with the protein transferrin underwent receptor-mediated endocytosis in cultured HeLa cells, and those dots that were labeled with immunomolecules recognized specific antibodies or antigens.

http://science.sciencemag.org/content/sci/281/5385/2016.full.pdf

Quantum Dot Bioconjugates for Ultrasensitive Nonisotopic Detection

Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as “core” for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf) yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification provides the bases for new analyses of the three-dimensional structure and for mutagenesis studies.

/pdf/multiple-amino-acid-sequence-alignment-nitrogenase-component-1l9bfdncvu.pdf

Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.

A partial amino-acid sequence of Bacillus subtilis 168 flagellin is presented. The region of unassigned sequence in this 304-residue polypeptide chain spans residues 158-173. Comparison of the 27-residue aminoterminal CNBr peptide of B. subtilis 168 flagellin with that derived from the flagellin of the serologically unrelated strain of B. subtilis, W23, shows only three conservative substitutions, whereas the 16-residue carboxyl-terminal peptides derived from these flagellins were identical. The comparison of the very limited sequence information available on the flagellins of Salmonella and Proteus with that on B. subtilis indicates homology between these proteins.

On the Amino-Acid Sequence of Flagellin from Bacillus subtilis 168: Comparison with Other Bacterial Flagellins

R-phycocyanin II (RPCII) is a recently discovered member of the phycocyanin family of photosynthetic light-harvesting proteins. Genes encoding the α and β subunits of RPCII were cloned and sequenced from marine Synechococcus sp. strains WH8020 and WH8103. The deduced amino acid sequences of RPCII were compared to two other types of phycocyanin, C-phycocyanin (CPC) and phycoerythrocyanin (PEC). These three types vary in the composition of their covalently bound bilin prosthetic groups. In terms of amino acid sequence identity RPCII is highly homologous to CPC and PEC, suggesting that the known three-dimensional structures of the latter two are representative of RPCII. Thus the amino acid residues contacting the three bilins of RPCII could be inferred and compared to those in CPC and PEC. Certain residues were identified among the three phycocyanins as possibly correlating with specific bilin isomers. In overall sequence RPCII and CPC are more homologous to one another than either is to PEC. This probably reflects functional homology in the roles of RPCII and CPC in the transfer of light energy to the core of the phycobilisome, a function not attributed to PEC. The genomes of Synechococcus sp. strains WH8020, WH8103 and WH7803 share homologous open reading frames in the vicinity of RPCII genes. The nucleotide sequence extending 3′ from RPCII genes in strain WH8020 revealed two open reading frames homologous to components of an αCPC phycocyanobilin lyase. These open reading frames may encode a lyase specific for the attachment of phycoerythrobilin to αRPCII.

Genes of the R-phycocyanin II locus of marine Synechococcus spp., and comparison of protein-chromophore interactions in phycocyanins differing in bilin composition

Publisher Summary Phycobiliproteins purified to homogeneity are very stable and can be stored for long periods without detectable change in aggregation state or spectroscopic properties. The amino acid sequences of numerous phycobiliproteins have been determined both directly and from analyses of cloned genes. On an average, these proteins contain about seven lysines per 100 residues and can be coupled through ɛ-amino groups to a variety of small molecules or macromolecules without any alteration in spectroscopic properties or the stability of the phycobiliprotein. Phycobiliprotein conjugates make possible fluorescence-based analyses of far higher sensitivity than that achievable with other fluorophores. Biotinylated phycoerythrin (1 ml) obtained in this manner is added slowly with stirring to 1 ml of 5 mg/ml avidin in the pH 6.8 phosphate buffer. The molar ratio of tetrameric avidin to phycoerythrin is 20. The mixture of phycoerythrin–biotin–avidin, biotin–phycoerythrin, unmodified phycoerythrin, and avidin is fractionated by high-performance liquid chromatography (HPLC) on a Varian G3000SW gel filtration column eluted with 200 mM sodium phosphate (pH 6.8).

Phycobiliprotein-avidin and phycobiliprotein-biotin conjugates.

This invention provides a class of phycoerythrins useful in diagnostic and detection protocols wherein a fluorescent label is required. The unique spectral properties of the phycoerythrins described herein provide for increased sensitivity and alternative uses in assays employing them.

Alexander N. Glazer

Papers

Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.

On the Amino-Acid Sequence of Flagellin from Bacillus subtilis 168: Comparison with Other Bacterial Flagellins

Genes of the R-phycocyanin II locus of marine Synechococcus spp., and comparison of protein-chromophore interactions in phycocyanins differing in bilin composition

Phycobiliprotein-avidin and phycobiliprotein-biotin conjugates.

Phycoerythrins useful in fluorescent conjugates