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  • 1
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 36 (1995), S. 43-51 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: During evolution, the effective interactions between residues in a protein can be adjusted through mutations to allow the protein to fold to its native structure on an adequate time scale. We seek to address the question: Are there some structures that can be better optimized than others? Using exhaustive enumeration of the compact conformations of short proteins confined to simple lattices, we find that the best structures are those that contain contacts rare in random structures, indicating the importance of nonlocal contacts for assisting the folding process. Certain structural motifs such as long β-hairpins, Greek-key motifs, and jelly rolls, commonly found in proteins of known structure, have a high degree of optimizability. Contrary to what might be expected, positive correlations between the various interactions reduce optimizability. The optimization procedure produces a correlated energy landscape, which might assist folding. © 1995 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 42 (1997), S. 427-438 
    ISSN: 0006-3525
    Keywords: protein folding ; molecular evolution ; lattice models ; fitness landscapes ; spin glasses ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular evolution may be considered as a walk in a multidimensional fitness landscape, where the fitness at each point is associated with features such as the function, stability, and survivability of these molecules. We present a simple model for the evolution of protein sequences on a landscape with a precisely defined fitness function. We use simple lattice models to represent protein structures, with the ability of a protein sequence to fold into the structure with lowest energy, quantified as the foldability, representing the fitness of the sequence. The foldability of the sequence is characterized based on the spin glass model of protein folding. We consider evolution as a walk in this foldability landscape and study the nature of the landscape and the resulting dynamics. Selective pressure is explicitly included in this model in the form of a minimum foldability requirement. We find that different native structures are not evenly distributed in interaction space, with similar structures and structures with similar optimal foldabilities clustered together. Evolving proteins marginally fulfill the selective criteria of foldability. As the selective pressure is increased, evolutionary trajectories become increasingly confined to “neutral networks,” where the sequence and the interactions can be significantly changed while a constant structure is maintained. © 1997 John Wiley & Sons, Inc. Biopoly 42: 427-438, 1997
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 3
    Publication Date: 1992-10-02
    Description: Some individuals infected with hepatitis C virus (HCV) experience multiple episodes of acute hepatitis. It is unclear whether these episodes are due to reinfection with HCV or to reactivation of the original virus infection. Markers of viral replication and host immunity were studied in five chimpanzees sequentially inoculated over a period of 3 years with different HCV strains of proven infectivity. Each rechallenge of a convalescent chimpanzee with the same or a different HCV strain resulted in the reappearance of viremia, which was due to infection with the subsequent challenge virus. The evidence indicates that HCV infection does not elicit protective immunity against reinfection with homologous or heterologous strains, which raises concerns for the development of effective vaccines against HCV.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Farci, P -- Alter, H J -- Govindarajan, S -- Wong, D C -- Engle, R -- Lesniewski, R R -- Mushahwar, I K -- Desai, S M -- Miller, R H -- Ogata, N -- New York, N.Y. -- Science. 1992 Oct 2;258(5079):135-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hepatitis Viruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1279801" target="_blank"〉PubMed〈/a〉
    Keywords: Acute Disease ; Aged ; Alanine Transaminase/biosynthesis ; Animals ; Base Sequence ; Hepacivirus/physiology ; Hepatitis Antibodies/biosynthesis ; Hepatitis C/*immunology ; Hepatitis C Antibodies ; Humans ; Immunity, Active ; Longitudinal Studies ; Molecular Sequence Data ; Pan troglodytes ; Polymerase Chain Reaction ; Sequence Homology ; Transcription, Genetic ; Viremia ; Virus Replication
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2012-03-24
    Description: A specific memory is thought to be encoded by a sparse population of neurons. These neurons can be tagged during learning for subsequent identification and manipulation. Moreover, their ablation or inactivation results in reduced memory expression, suggesting their necessity in mnemonic processes. However, the question of sufficiency remains: it is unclear whether it is possible to elicit the behavioural output of a specific memory by directly activating a population of neurons that was active during learning. Here we show in mice that optogenetic reactivation of hippocampal neurons activated during fear conditioning is sufficient to induce freezing behaviour. We labelled a population of hippocampal dentate gyrus neurons activated during fear learning with channelrhodopsin-2 (ChR2) and later optically reactivated these neurons in a different context. The mice showed increased freezing only upon light stimulation, indicating light-induced fear memory recall. This freezing was not detected in non-fear-conditioned mice expressing ChR2 in a similar proportion of cells, nor in fear-conditioned mice with cells labelled by enhanced yellow fluorescent protein instead of ChR2. Finally, activation of cells labelled in a context not associated with fear did not evoke freezing in mice that were previously fear conditioned in a different context, suggesting that light-induced fear memory recall is context specific. Together, our findings indicate that activating a sparse but specific ensemble of hippocampal neurons that contribute to a memory engram is sufficient for the recall of that memory. Moreover, our experimental approach offers a general method of mapping cellular populations bearing memory engrams.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331914/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331914/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Xu -- Ramirez, Steve -- Pang, Petti T -- Puryear, Corey B -- Govindarajan, Arvind -- Deisseroth, Karl -- Tonegawa, Susumu -- P50 MH058880/MH/NIMH NIH HHS/ -- P50 MH058880-10/MH/NIMH NIH HHS/ -- P50-MH58880/MH/NIMH NIH HHS/ -- R01 MH078821/MH/NIMH NIH HHS/ -- R01 MH078821-17/MH/NIMH NIH HHS/ -- R01-MH078821/MH/NIMH NIH HHS/ -- England -- Nature. 2012 Mar 22;484(7394):381-5. doi: 10.1038/nature11028.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉RIKEN-MIT Center for Neural Circuit Genetics at the Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22441246" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacterial Proteins/genetics/metabolism ; Conditioning (Psychology)/physiology/radiation effects ; Dentate Gyrus/cytology/physiology/radiation effects ; Fear/*physiology/*radiation effects ; Female ; Freezing Reaction, Cataleptic/physiology/radiation effects ; Gene Expression Regulation ; Hippocampus/cytology/*physiology/*radiation effects ; Light ; Luminescent Proteins/genetics/metabolism ; Male ; Mental Recall/*radiation effects ; Mice ; Mice, Transgenic ; Rhodopsin/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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