Protein comparison and classification: a differential geometric approach.

abstract：:Stabilization of neuronal activity by homeostatic control systems is fundamental for proper functioning of neural circuits. Failure in neuronal homeostasis has been hypothesized to underlie common pathophysiological mechanisms in a variety of brain disorders. However, the key molecules regulating homeostasis in centra...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Vertkin I,Styr B,Slomowitz E,Ofir N,Shapira I,Berner D,Fedorova T,Laviv T,Barak-Broner N,Greitzer-Antes D,Gassmann M,Bettler B,Lotan I,Slutsky I

更新日期：2015-06-23 00:00:00

abstract：:The protein-protein interaction (PPI) network is crucial for cellular information processing and decision-making. With suitable inputs, PPI networks drive the cells to diverse functional outcomes such as cell proliferation or cell death. Here, we characterize the structural controllability of a large directed human PP...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Vinayagam A,Gibson TE,Lee HJ,Yilmazel B,Roesel C,Hu Y,Kwon Y,Sharma A,Liu YY,Perrimon N,Barabási AL

更新日期：2016-05-03 00:00:00

abstract：:NaeI is a remarkable type II restriction endonuclease. It must bind two recognition sequences to cleave DNA, forms a covalent protein-DNA intermediate, and is only 1 aa change away from topoisomerase and recombinase activity. The latter activities apparently derive from reactivation of a cryptic DNA ligase active site...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Colandene JD,Topal MD

更新日期：1998-03-31 00:00:00

abstract：:Saccharomyces cerevisiae has a complex system for switching the mating type of haploid cells, requiring the genome to have three mating-type (MAT)-like loci and a mechanism for silencing two of them. How this system originated is unknown, because the three-locus system is present throughout the family Saccharomycetace...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Hanson SJ,Byrne KP,Wolfe KH

更新日期：2014-11-11 00:00:00

abstract：:Cancer stem cells (CSCs) sustain tumor growth through their ability to self-renew and to generate differentiated progeny. These functions endow CSCs with the potential to initiate secondary tumors bearing characteristics similar to those of the parent. Recently the hair follicle stem cell marker CD34 was used to purif...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Schober M,Fuchs E

更新日期：2011-06-28 00:00:00

abstract：:The presynaptic plasma membrane protein SNAP-25 (synaptosome-associated protein of 25 kDa) has been implicated as one of several neural-specific components that direct constitutive fusion mechanisms to the regulated vesicle trafficking and exocytosis of neurotransmitter release. There exist two alternatively spliced i...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Bark IC,Hahn KM,Ryabinin AE,Wilson MC

更新日期：1995-02-28 00:00:00

abstract：:Stress-induced structural remodeling in the adult hippocampus, involving debranching and shortening of dendrites and suppression of neurogenesis, provides a cellular basis for understanding the impairment of neural plasticity in the human hippocampus in depressive illness. Accordingly, reversal of structural remodelin...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Czéh B,Michaelis T,Watanabe T,Frahm J,de Biurrun G,van Kampen M,Bartolomucci A,Fuchs E

更新日期：2001-10-23 00:00:00

abstract：:We describe a role for ECM as a biosensor for inflammatory microenvironments that plays a critical role in peripheral immune tolerance. We show that hyaluronan (HA) promotes induction of Foxp3- IL-10-producing regulatory T cells (TR1) from conventional T-cell precursors in both murine and human systems. This is, to ou...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Bollyky PL,Wu RP,Falk BA,Lord JD,Long SA,Preisinger A,Teng B,Holt GE,Standifer NE,Braun KR,Xie CF,Samuels PL,Vernon RB,Gebe JA,Wight TN,Nepom GT

更新日期：2011-05-10 00:00:00

abstract：:Most human tumors are clonal in origin, although the cells may be diverse in their properties. Since the tumors evolve through progressive stages over decades of time, it is possible that the conditions that induced the tumor transform many cells, but that selective overgrowth of the fastest growing lead to a clonal p...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Yao A,Rubin H

更新日期：1993-11-15 00:00:00

abstract：:The formation of a fracture network is a key process for many geophysical and industrial practices from energy resource recovery to induced seismic management. We focus on the initial stage of a fracture network formation using experiments on the symmetric coalescence of two equal coplanar, fluid-driven, penny-shaped ...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： O'Keeffe NJ,Zheng Z,Huppert HE,Linden PF

更新日期：2018-10-09 00:00:00

abstract：:Renal cells isolated from vitamin D-deficient chicks had an increased Na+-dependent phosphate uptake when preincubated with 1,25-dihydroxycholecalciferol [1,25-(OH)2D3]. Phosphate uptake in the absence of Na+ and methyl alpha-glucoside uptake dependent on Na+ were not affected. Phosphate uptake was stimulated 15% by 0...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Liang CT,Barnes J,Balakir R,Cheng L,Sacktor B

更新日期：1982-06-01 00:00:00

abstract：:Pyrimethamine (Pyr) targets dihydrofolate reductase of Plasmodium vivax (PvDHFR) as well as other malarial parasites, but its use as antimalarial is hampered by the widespread high resistance. Comparison of the crystal structures of PvDHFR from wild-type and the Pyr-resistant (SP21, Ser-58 --> Arg + Ser-117 --> Asn) s...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Kongsaeree P,Khongsuk P,Leartsakulpanich U,Chitnumsub P,Tarnchompoo B,Walkinshaw MD,Yuthavong Y

更新日期：2005-09-13 00:00:00

abstract：:Polymersomes, which are stable and robust vesicles made of block copolymer amphiphiles, are good candidates for drug carriers or micro/nanoreactors. Polymer chemistry enables almost unlimited molecular design of responsive polymersomes whose degradation upon environmental changes has been used for the slow release of ...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Mabrouk E,Cuvelier D,Brochard-Wyart F,Nassoy P,Li MH

更新日期：2009-05-05 00:00:00

abstract：:We study inverse statistical mechanics: how can one design a potential function so as to produce a specified ground state? In this article, we show that unexpectedly simple potential functions suffice for certain symmetrical configurations, and we apply techniques from coding and information theory to provide mathemat...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Cohn H,Kumar A

更新日期：2009-06-16 00:00:00

abstract：:The phylogenetic affinities of the grass family (Poaceae) have long been debated. The chloroplast genomes of at least some grasses have been known to possess three inversions relative to the typical gene arrangement found in most flowering plants. We have surveyed for the presence of these inversions in grasses and ot...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Doyle JJ,Davis JI,Soreng RJ,Garvin D,Anderson MJ

更新日期：1992-08-15 00:00:00

abstract：:In the presence of the S polypeptide, maize chloroplast DNA-dependent RNA polymerase preferentially transcribes sequences within the 2200-nucleotide-pair-long maize chloroplast chromosome fragment Eco [unk] from a supercoiled chimeric plasmid cloned in Escherichia coli [Jolly, S. O. & Bogorad, L. (1980) Proc. Natl. Ac...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Schwarz Z,Jolly SO,Steinmetz AA,Bogorad L

更新日期：1981-06-01 00:00:00

abstract：:The global configuration of individual, surface-adsorbed molecules of the giant muscle protein titin, labeled with rhodamine conjugates, was followed with confocal microscopy. Fluorescence-emission intensity was reduced because of self-quenching caused by the close spacing between rhodamine dye molecules that formed d...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Grama L,Somogyi B,Kellermayer MS

更新日期：2001-12-04 00:00:00

abstract：:Estimation of gene diversity (heterozygosity) at 1442 single-nucleotide polymorphism (SNP) loci in an ethnically diverse sample of humans revealed consistently reduced gene diversities at SNP loci causing amino acid changes, particularly those causing amino acid changes predicted to be disruptive to protein structure....

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Hughes AL,Packer B,Welch R,Bergen AW,Chanock SJ,Yeager M

更新日期：2003-12-23 00:00:00

abstract：:The template for transcription and replication of negative-stranded RNA viruses is a ribonucleoprotein structure, the nucleocapsid. We have developed a system that supports assembly of the negative-stranded RNA genome of a defective interfering (DI) particle of vesicular stomatitis virus (VSV) into a nucleocapsid in v...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Mirakhur B,Peluso RW

更新日期：1988-10-01 00:00:00

abstract：:A 2.5-fold stimulation of cyclic AMP cellular content is measured 60 sec after addition of 100 nM synthetic ovine corticotropin-releasing factor (C-RF; corticoliberin) to rat anterior pituitary cells in culture. A maximal response of cyclic AMP content at 400% above control is observed between 2 and 30 min after addit...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Giguère V,Labrie F,Côté J,Coy DH,Sueiras-Diaz J,Schally AV

更新日期：1982-06-01 00:00:00

abstract：:This is a multinanosecond molecular dynamics study of a bio-nano complex formed by a carbon nanoparticle, a buckyball C(60), and a biological molecule, an antibody, with high binding affinity and specificity. In the simulation, the ball is completely desolvated by the binding site of the antibody by means of a nearly ...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Noon WH,Kong Y,Ma J

更新日期：2002-04-30 00:00:00

abstract：:The conformation of DNA bound in nucleosomes depends on the DNA sequence. Questions such as how nucleosomes are positioned and how they potentially bind sequence-dependent nuclear factors require near-atomic resolution structures of the nucleosome core containing different DNA sequences; despite this, only the DNA for...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Frouws TD,Duda SC,Richmond TJ

更新日期：2016-02-02 00:00:00

abstract：:This paper explores the explanations for, and consequences of, the early appearance of food production outside the Fertile Crescent of Southwest Asia, where it originated in the 10th/9th millennia cal BC. We present evidence that cultivation appeared in Central Anatolia through adoption by indigenous foragers in the m...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Baird D,Fairbairn A,Jenkins E,Martin L,Middleton C,Pearson J,Asouti E,Edwards Y,Kabukcu C,Mustafaoğlu G,Russell N,Bar-Yosef O,Jacobsen G,Wu X,Baker A,Elliott S

更新日期：2018-04-03 00:00:00

abstract：:We introduce a quantitative framework for assessing the generation of crossovers in DNA shuffling experiments. The approach uses free energy calculations and complete sequence information to model the annealing process. Statistics obtained for the annealing events then are combined with a reassembly algorithm to infer...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Moore GL,Maranas CD,Lutz S,Benkovic SJ

更新日期：2001-03-13 00:00:00

abstract：:Bright, photostable, and nontoxic fluorescent contrast agents are critical for biological imaging. "Self-healing" dyes, in which triplet states are intramolecularly quenched, enable fluorescence imaging by increasing fluorophore brightness and longevity, while simultaneously reducing the generation of reactive oxygen ...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Pati AK,El Bakouri O,Jockusch S,Zhou Z,Altman RB,Fitzgerald GA,Asher WB,Terry DS,Borgia A,Holsey MD,Batchelder JE,Abeywickrama C,Huddle B,Rufa D,Javitch JA,Ottosson H,Blanchard SC

更新日期：2020-09-29 00:00:00

abstract：:The immunoglobulin heavy-chain-associated tetrapeptide, tuftsin (Thr-Lys-Pro-Arg), known for its phagocytosis-stimulating activity, was found to augment the antigen-specific, macrophage-dependent education of T lymphocytes. The investigation of stereospecific characteristics of the tetrapeptide, by use of structural a...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Tzehoval E,Segal S,Stabinsky Y,Fridkin M,Spirer Z,Feldman M

更新日期：1978-07-01 00:00:00

abstract：:Primary tumors secrete factors that alter the microenvironment of distant organs, rendering those organs as fertile soil for subsequent metastatic cancer cell colonization. Although the lungs are exposed to these factors ubiquitously, lung metastases usually develop as a series of discrete lesions. The underlining mol...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Hiratsuka S,Goel S,Kamoun WS,Maru Y,Fukumura D,Duda DG,Jain RK

更新日期：2011-03-01 00:00:00

abstract：:Maintaining the fidelity of nascent peptide chain (NP) synthesis is essential for proteome integrity and cellular health. Ribosome-associated quality control (RQC) serves to resolve stalled translation, during which untemplated Ala/Thr residues are added C terminally to stalled peptide, as shown during C-terminal Ala ...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Li S,Wu Z,Tantray I,Li Y,Chen S,Dong J,Glynn S,Vogel H,Snyder M,Lu B

更新日期：2020-10-06 00:00:00

abstract：:The generation of toxic oligomers during the aggregation of the amyloid-β (Aβ) peptide Aβ42 into amyloid fibrils and plaques has emerged as a central feature of the onset and progression of Alzheimer's disease, but the molecular pathways that control pathological aggregation have proved challenging to identify. Here, ...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Cohen SI,Linse S,Luheshi LM,Hellstrand E,White DA,Rajah L,Otzen DE,Vendruscolo M,Dobson CM,Knowles TP

更新日期：2013-06-11 00:00:00

abstract：:Antibody-coated latex beads (Ab-beads) were attached to Leptospira interrogans serovars illini 3055 and icterohaemorrhagiae SC1157. The movement of the Ab-beads relative to the motion of the cells was observed by direct darkfield microscopy or was recorded on videotape. When the Ab-beads were attached to the front end...

journal_title：Proceedings of the National Academy of Sciences of the United States of America

authors： Charon NW,Lawrence CW,O'Brien S

更新日期：1981-11-01 00:00:00