J.A. Camarero et al., "Peptide chemical ligation inside living cells: In vivo generation of a circular protein domain," Bioorganic and Medicinal Chemistry, 9[9]:2479-84, September 2001.
F1000 Rating: Recommended
"To investigate whether chemo-selective peptide ligations work in vivo, the authors demonstrate the in vivo head-to-tail cyclization of a bioactive SH3 domain using native chemical ligation. The protein precursor was constructed using a clever combination of an intein-fusion protein and cleavage of an N-terminal Met-Cys-Gly motif by an endogenous protease. Such cyclic proteins and peptides may be applied to peptide libraries or to improve the stability of
cellular proteins." "To investigate whether chemo-selective peptide ligations work in vivo, the authors demonstrate the in vivo head-to-tail cyclization of a bioactive SH3 domain using native chemical ligation. The protein precursor was constructed using a clever combination of an intein-fusion protein and cleavage of an N-terminal Met-Cys-Gly motif by an endogenous protease. Such cyclic proteins and peptides may be applied to peptide libraries or to improve the stability of
Structural Biology
S. Ghaemmaghami, T.G. Oas, "Quantitative protein stability measurement in vivo," Nature Structural Biology, 8[10]:879-82, October 2001.
F1000 Rating: Must Read
"The authors present the first quantitative comparison between the stability of a protein in vitro and in the cytoplasm of Escherichia coli using amide hydrogen exchange detected by MALDI mass spectrometry, a procedure they call SUPREX. Their results indicate that the thermodynamic stability of their model protein lambda repressor within the cell is the same as for the purified protein in aqueous buffer. This in vivo method holds great promise, at least for small proteins, and will be useful for applications where intracellular stability information is needed."
"The authors present the first quantitative comparison between the stability of a protein in vitro and in the cytoplasm of Escherichia coli using amide hydrogen exchange detected by MALDI mass spectrometry, a procedure they call SUPREX. Their results indicate that the thermodynamic stability of their model protein lambda repressor within the cell is the same as for the purified protein in aqueous buffer. This in vivo method holds great promise, at least for small proteins, and will be useful for applications where intracellular stability information is needed."
Developmental Biology
S. Zhou et al., "The ABC transporter Bcrp1/ABCG2 is expressed in a wide variety of stem cells and is a molecular determinant of the side-population phenotype," Nature Medicine, 7[9]:1028-34, September 2001.
F1000 Rating: Exceptional
"This fascinating study defines the molecular basis for one functional characteristic of primitive stem cells in multiple species, the so-called "side population" defined by efflux of the fluorescent Hoechst 33342 molecule. An ABC transporter protein previously identified in epithelial cancer cells conferred the side population phenotype when expressed in cells, and overexpression blocked differentiation of hematopoietic stem cells. Importantly, separation of subsets of cells from two embryonic stem cell lines based on the side population phenotype resulted in higher chimerism in animals derived from blastocysts injected with side population cells compared to those receiving the non-side population subset. This study defines an important mechanism in stem cell biology that may help define how self-renewal of stem cells is regulated."
"This fascinating study defines the molecular basis for one functional characteristic of primitive stem cells in multiple species, the so-called "side population" defined by efflux of the fluorescent Hoechst 33342 molecule. An ABC transporter protein previously identified in epithelial cancer cells conferred the side population phenotype when expressed in cells, and overexpression blocked differentiation of hematopoietic stem cells. Importantly, separation of subsets of cells from two embryonic stem cell lines based on the side population phenotype resulted in higher chimerism in animals derived from blastocysts injected with side population cells compared to those receiving the non-side population subset. This study defines an important mechanism in stem cell biology that may help define how self-renewal of stem cells is regulated."
Genomics
N. Winssinger et al., "From split-pool libraries to spatially addressable microarrays and its application to functional proteomic profiling," Angewandte Chemie International Edition in English, 40:3152-55, 2001.
F1000 Rating: Must Read
"The paper describes a new technique that utilizes the ability of peptide nucleic acid (PNA) to bind strongly to microarrays of encoding tags in the form of DNA to pull out high affinity ligands for different proteins in mixtures. Small molecules are synthesized simultaneously with an encoding PNA string and incubated with target proteins in solution. The complexes are isolated by simple dialysis and structure of active ligands decoded by binding to complementary DNA codes on the microchip. Detection of protein binding by differential fluorescence labeled target proteins allows the distinction between binding activities for several targets. The technique is simple, general and robust, although, as admitted by the authors, the limit for direct detection of binding is still low."
"The paper describes a new technique that utilizes the ability of peptide nucleic acid (PNA) to bind strongly to microarrays of encoding tags in the form of DNA to pull out high affinity ligands for different proteins in mixtures. Small molecules are synthesized simultaneously with an encoding PNA string and incubated with target proteins in solution. The complexes are isolated by simple dialysis and structure of active ligands decoded by binding to complementary DNA codes on the microchip. Detection of protein binding by differential fluorescence labeled target proteins allows the distinction between binding activities for several targets. The technique is simple, general and robust, although, as admitted by the authors, the limit for direct detection of binding is still low."
Bioinformatics
E. Kraemer et al., "An analysis of gene- finding programs for Neurospora crassa," Bioinformatics, 17:901-12, October 2001.
F1000 Rating: Recommended
"This paper evaluates the relative success of gene finding programs for the fungus Neurospora crassa, the first filamentous fungus with an essentially complete DNA sequence to be made available on a publicly accessible database. Gene finding from DNA sequence data is currently imprecise as the rules are imperfectly understood and clearly vary across biota. For the present, those seeking to annotate parts of this genome should not rely on the predictions from any of the available programs."
"This paper evaluates the relative success of gene finding programs for the fungus Neurospora crassa, the first filamentous fungus with an essentially complete DNA sequence to be made available on a publicly accessible database. Gene finding from DNA sequence data is currently imprecise as the rules are imperfectly understood and clearly vary across biota. For the present, those seeking to annotate parts of this genome should not rely on the predictions from any of the available programs."
Medical Genetics
H. Okuda et al., "The von Hippel-Lindau tumor suppressor protein mediates ubiquitination of activated atypical protein kinase C," Journal of Biological Chemistry, 276:43611-7, November 2001.
F1000 Rating: Recommended
"The von Hippel-Lindau tumor suppressor gene (VHL) has a critical role in regulating proteolysis of the hypoxia inducible factor (HIF) transcription factors, but to date the known functions of the VHL protein do not adequately explain its tumor suppressor activity; however, this paper sheds light of this by demonstrating that it targets an atypical protein kinase C (PKC*). The authors report this novel target, PKC*, is ubiquitinated in a VHL-dependent manner."
"The von Hippel-Lindau tumor suppressor gene (VHL) has a critical role in regulating proteolysis of the hypoxia inducible factor (HIF) transcription factors, but to date the known functions of the VHL protein do not adequately explain its tumor suppressor activity; however, this paper sheds light of this by demonstrating that it targets an atypical protein kinase C (PKC*). The authors report this novel target, PKC*, is ubiquitinated in a VHL-dependent manner."
Immunology
M. Zhou et al., "Friend of GATA-1 represses GATA-3-dependent activity in CD4(+) T cells," Journal of Experimental Medicine, 194:1461-71, November 19, 2001.
F1000 Rating: Must Read
"This paper identifies Friend of GATA-1 (FOG-1) as a potential regulator of the transcription factor GATA-3, a key regulator that directs CD4-T cell differentiation towards the pro-allergenic Th2 phenotype. FOG-1 was originally identified as a repressor of GATA transcription factor activity during hematopoiesis, particularly in red blood cell and platelet development. Here, using retroviral mediated overexpression of FOG-1 in either naive CD4 cells or in Th2 cells, these investigators show that FOG-1 can down-regulate GATA-3-dependent functions in mature Th2 cells and also repress the differentiation of Th2 cells from naive precursors. This defines FOG-1 as a potential physiologically important regulator of Th2 cell development and identifies it as a therapeutic target for modulating the balance of Th1 and Th2 cells."
"This paper identifies Friend of GATA-1 (FOG-1) as a potential regulator of the transcription factor GATA-3, a key regulator that directs CD4-T cell differentiation towards the pro-allergenic Th2 phenotype. FOG-1 was originally identified as a repressor of GATA transcription factor activity during hematopoiesis, particularly in red blood cell and platelet development. Here, using retroviral mediated overexpression of FOG-1 in either naive CD4 cells or in Th2 cells, these investigators show that FOG-1 can down-regulate GATA-3-dependent functions in mature Th2 cells and also repress the differentiation of Th2 cells from naive precursors. This defines FOG-1 as a potential physiologically important regulator of Th2 cell development and identifies it as a therapeutic target for modulating the balance of Th1 and Th2 cells."
