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761
Dynamic Programming and Clique Based Approaches for Protein Threading with Profiles and Constraints ∗
, 2006
"... SUMMARY The protein threading problem with profiles is known to be efficiently solvable using dynamic programming. In this paper, we consider a variant of the protein threading problem with profiles in which constraints on distances between residues are given. We prove that protein threading with pr ..."
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accuracy of the target sequence and the template structure. Moreover, these results also show that BBDPTHREAD is in general faster than CLIQUETHREAD for larger size proteins whereas CLIQUETHREAD is useful if there does not exist a feasible threading. key words: maximum edge weight clique, dynamic
Native C-Reactive Protein Increases Whereas Modified C-Reactive Protein Reduces Atherosclerosis in
"... Background—C-reactive protein (CRP) may have proatherogenic but also vasoprotective properties. We tested the hypothesis that the configuration of CRP (pentameric, or native [nCRP], versus monomeric, or modified [mCRP]) determines these different characteristics in an in vivo model. Methods and Resu ..."
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Background—C-reactive protein (CRP) may have proatherogenic but also vasoprotective properties. We tested the hypothesis that the configuration of CRP (pentameric, or native [nCRP], versus monomeric, or modified [mCRP]) determines these different characteristics in an in vivo model. Methods
Auxin regulates the initiation and radial position of plant organs
- The Plant Cell
, 2000
"... Leaves originate from the shoot apical meristem, a small mound of undifferentiated tissue at the tip of the stem. Leaf formation begins with the selection of a group of founder cells in the so-called peripheral zone at the flank of the mer-istem, followed by the initiation of local growth and finall ..."
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Cited by 85 (8 self)
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in the radial dimension, whereas in the apical–basal dimension, organ formation always occurred at a fixed distance from the summit of the meristem. We pro-pose that auxin determines the radial position and the size of lateral organs but not the apical–basal position or the identity of the induced structures.
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion
- PLoS Biol
, 2004
"... Primary microcephaly (MCPH) is a neurodevelopmental disorder characterized by global reduction in cerebral cortical volume. The microcephalic brain has a volume comparable to that of early hominids, raising the possibility that some MCPH genes may have been evolutionary targets in the expansion of t ..."
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Cited by 44 (3 self)
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of the cerebral cortex in mammals and especially primates. Mutations in ASPM, which encodes the human homologue of a fly protein essential for spindle function, are the most common known cause of MCPH. Here we have isolated large genomic clones containing the complete ASPM gene, including promoter regions
Automated design of the surface positions of protein helices
- Protein Sci
, 1997
"... Using a protein design algorithm that quantitatively considers side-chain interactions, the design of surface residues of (Y helices was examined. Three scoring functions were tested: a hydrogen-bond potential, a hydrogen-bond potential in conjunction with a penalty for uncompensated burial of polar ..."
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Cited by 45 (9 self)
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peptides were synthesized and characterized by circular dichroism spectroscopy and size exclusion chromatography. The designed peptides were dimeric and nearly 100 % helical at 1 "C, with melting temperatures from 69-72 "C, over 12 "C higher than GCNCpl, whereas a random hydrophilic sequence
Sizing the Protein Translocation Pathway of Colicin Ia Channels
"... abstract The bacterial toxin colicin Ia forms voltage-gated channels in planar lipid bilayers. The toxin consists of three domains, with the carboxy-terminal domain (C-domain) responsible for channel formation. The C-domain contributes four membrane-spanning segments and a 68-residue translocated se ..."
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Cited by 1 (0 self)
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segment to the open channel, whereas the upstream domains and the amino-terminal end of the C-domain stay on the cis side of the membrane. The isolated C-domain, lacking the two upstream domains, also forms channels; however, the amino terminus and one of the normally membrane-spanning segments can move
Roles of LAP2 proteins in nuclear assembly and DNA replication: truncated LAP2� proteins alter lamina assembly, envelope formation, nuclear size, and DNA replication efficiency in Xenopus laevis extracts
- J. Cell
, 1999
"... Abstract. Humans express three major splicing isoforms of LAP2, a lamin- and chromatin-binding nuclear protein. LAP2 � and � are integral membrane proteins, whereas � is intranuclear. When truncated recombinant human LAP2 � proteins were added to cell-free Xenopus laevis nuclear assembly reactions a ..."
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Cited by 27 (2 self)
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Abstract. Humans express three major splicing isoforms of LAP2, a lamin- and chromatin-binding nuclear protein. LAP2 � and � are integral membrane proteins, whereas � is intranuclear. When truncated recombinant human LAP2 � proteins were added to cell-free Xenopus laevis nuclear assembly reactions
Involucrin synthesis is correlated with cell size in human epidermal cultures
- J. Cell BioL
, 1981
"... ABSTRACT Late in terminal differentiation, human epidermal keratinocytes form an insoluble protein envelope on the cytoplasmic side of the plasma membrane. Involucrin, a soluble protein precursor of the envelope, is synthesized at an earlier stage of differentiation, both in the natural epithelium a ..."
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Cited by 22 (3 self)
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and in cultured keratinocytes. Because keratinocytes are known to enlarge during differentiation, we looked for a correlation between involucrin synthesis and cell size, using antiserum raised against the purified protein. We found that virtually no cultured epidermal keratinocytes with a diameter <_14 ftm
Protein diffusion in living skeletal muscle fibers: dependence on protein size, fiber type, and contraction
- Biophys J
"... ABSTRACT Sarcoplasmic protein diffusion was studied under different conditions, using microinjection in combination with microspectrophotometry. Six globular proteins with molecular masses between 12 and 3700 kDa, with diameters from 3 to 30 nm, were used for the experiments. Proteins were injected ..."
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Cited by 13 (0 self)
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I fibers). Measurements of D for myoglobin at 37°C in addition to 22°C led to a Q10 of 1.46 for this temperature range. For the larger proteins catalase (diameter 10.5 nm) and ferritin (diameter 12.2 nm), a decrease in D to �1/20 and �1/50 of that in water was observed, whereas no diffusive flux
Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey,
- Structure
, 2000
"... Background: Proteins from thermophilic organisms usually show high intrinsic thermal stability but have structures that are very similar to their mesophilic homologues. From prevous studies it is difficult to draw general conclusions about the structural features underlying the increased thermal st ..."
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Cited by 50 (1 self)
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quality control of the structures used and the size of the data set. Conclusions: Different protein families adapt to higher temperatures by different sets of structural devices. Regarding the structural parameters, the only generally observed rule is an increase in the number of ion pairs with increasing
Results 1 - 10
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761