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Journal articles on the topic 'Amino acids - Structure'

Author: Grafiati

Published: 4 June 2021

Last updated: 13 February 2022

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1

Athmani, Hamza, and Nourreedine Benali-Cherif. "Structure and thermal analysis of amino acids." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C989. http://dx.doi.org/10.1107/s205327331409010x.

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The twenty amino acids are chemical compounds having two functional groups (carboxyl:-COOH, amine:-NH2) and an asymmetric carbon (except glycine). They are amphoteric and can exist as zwitterion. Because of the reactivity of amino acids (esterification, amidation, N-alkylisation, N-arylation, protonation), and their conformation (aliphatic, aromatic) chemical, properties (acid, base, and / or hydroxylated, solubility), and physical properties (absorbance, NLO), our laboratory contribute to the study (synthesis and X ray single crystal structures) of new organic-inorganic hybrid compounds which

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2

RAWLS, REBECCA. "Chiral Amino Acids Alter Mineral Structure." Chemical & Engineering News 79, no. 25 (2001): 11. http://dx.doi.org/10.1021/cen-v079n025.p011a.

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3

Nikiforov, L. A., M. V. Belousov, and N. S. Fursa. "Study of amino-acid structure Lemna minor L." Bulletin of Siberian Medicine 10, no. 5 (2011): 74–77. http://dx.doi.org/10.20538/1682-0363-2011-5-74-77.

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For the first time qualitative and quantitative amino-acid structure Lemna minor L. is studied with use of a highly effective liquid chromatography. Presence 18 proteinogennic amino acids, including 8 irreplaceable is established. The sum of replaceable amino acids of a duckweed small is presented monoaminocarboxylic,monoaminodicarboxylic, diaminomonocarboxylic and heterocyclic acids. Irreplaceable amino acids are presented monoaminomonocarboxylic and diaminomonocarboxylic by acids.

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4

Koehl, P., and M. Levitt. "Structure-based conformational preferences of amino acids." Proceedings of the National Academy of Sciences 96, no. 22 (1999): 12524–29. http://dx.doi.org/10.1073/pnas.96.22.12524.

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5

Tsai, Ruey-Shiuan, Bernard Testa, Nabil El Tayar, and Pierre-Alain Carrupt. "Structure–lipophilicity relationships of zwitterionic amino acids." J. Chem. Soc., Perkin Trans. 2, no. 11 (1991): 1797–802. http://dx.doi.org/10.1039/p29910001797.

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6

Wang, P., M. Reed, Y. Wang, et al. "p53 domains: structure, oligomerization, and transformation." Molecular and Cellular Biology 14, no. 8 (1994): 5182–91. http://dx.doi.org/10.1128/mcb.14.8.5182.

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Wild-type p53 forms tetramers and multiples of tetramers. Friedman et al. (P. N. Friedman, X. B. Chen, J. Bargonetti, and C. Prives, Proc. Natl. Acad. Sci. USA 90:3319-3323, 1993) have reported that human p53 behaves as a larger molecule during gel filtration than it does during sucrose gradient sedimentation. These differences argue that wild-type p53 has a nonglobular shape. To identify structural and oligomerization domains in p53, we have investigated the physical properties of purified segments of p53. The central, specific DNA-binding domain within murine amino acids 80 to 320 and human

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7

Wang, P., M. Reed, Y. Wang, et al. "p53 domains: structure, oligomerization, and transformation." Molecular and Cellular Biology 14, no. 8 (1994): 5182–91. http://dx.doi.org/10.1128/mcb.14.8.5182-5191.1994.

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Wild-type p53 forms tetramers and multiples of tetramers. Friedman et al. (P. N. Friedman, X. B. Chen, J. Bargonetti, and C. Prives, Proc. Natl. Acad. Sci. USA 90:3319-3323, 1993) have reported that human p53 behaves as a larger molecule during gel filtration than it does during sucrose gradient sedimentation. These differences argue that wild-type p53 has a nonglobular shape. To identify structural and oligomerization domains in p53, we have investigated the physical properties of purified segments of p53. The central, specific DNA-binding domain within murine amino acids 80 to 320 and human

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8

Heinicke, Joachim, Joanna Lach, Kaleswara R. Basvani, Normen Peulecke, Peter G. Jones та Martin Köckerling. "α-Phosphino Amino Acids: Synthesis, Structure, and Reactivity". Phosphorus, Sulfur, and Silicon and the Related Elements 186, № 4 (2011): 666–77. http://dx.doi.org/10.1080/10426507.2010.514485.

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9

Smith, Martin D., Timothy D. W. Claridge, George W. J. Fleet, George E. Tranter, and Mark S. P. Sansom. "Secondary structure in oligomers of carbohydrate amino acids." Chemical Communications, no. 18 (1998): 2041–42. http://dx.doi.org/10.1039/a805401k.

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10

CHEON, MOOKYUNG, MUYOUNG HEO, IKSOO CHANG, and CHOONGRAK KIM. "CLASSIFICATIONS OF AMINO ACIDS IN PROTEINS BY THE SELF-ORGANIZING MAP." International Journal of Modern Physics C 16, no. 10 (2005): 1609–16. http://dx.doi.org/10.1142/s0129183105008175.

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We present the clustering properties of amino acids, which are building blocks of proteins, according to their physico-chemical characters. To classify the 20 kinds of amino acids, we employ a Self-Organizing Map (SOM) analysis for the Miyazawa-Jernigan (MJ) pairwise-contact matrix, the Environment-dependent One-body energy Parameters (EOP) and the one-body energy parameters incorporating the Ramachandran angle information (EOPR) over the EOP in proteins. We provide the new result of the SOM clustering for amino acids based on the EOPR and compare that with those from the MJ and the EOP matrix

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11

Rogers, Joseph M., Toby Passioura, and Hiroaki Suga. "Nonproteinogenic deep mutational scanning of linear and cyclic peptides." Proceedings of the National Academy of Sciences 115, no. 43 (2018): 10959–64. http://dx.doi.org/10.1073/pnas.1809901115.

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High-resolution structure–activity analysis of polypeptides requires amino acid structures that are not present in the universal genetic code. Examination of peptide and protein interactions with this resolution has been limited by the need to individually synthesize and test peptides containing nonproteinogenic amino acids. We describe a method to scan entire peptide sequences with multiple nonproteinogenic amino acids and, in parallel, determine the thermodynamics of binding to a partner protein. By coupling genetic code reprogramming to deep mutational scanning, any number of amino acids ca

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12

Cao, Chen, Lincong Wang, Xiaoyang Chen, Shuxue Zou, Guishen Wang, and Shutan Xu. "Amino Acids in Nine Ligand-Prefer Ramachandran Regions." BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/757495.

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Several secondary structures, such asπ-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts,

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13

van Beusekom, Bart, George Damaskos, Maarten L. Hekkelman, et al. "LAHMA: structure analysis through local annotation of homology-matched amino acids." Acta Crystallographica Section D Structural Biology 77, no. 1 (2021): 28–40. http://dx.doi.org/10.1107/s2059798320014473.

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Comparison of homologous structure models is a key step in analyzing protein structure. With a wealth of homologous structures, comparison becomes a tedious process, and often only a small (user-biased) selection of data is used. A multitude of structural superposition algorithms are then typically used to visualize the structures together in 3D and to compare them. Here, the Local Annotation of Homology-Matched Amino acids (LAHMA) website (https://lahma.pdb-redo.eu) is presented, which compares any structure model with all of its close homologs from the PDB-REDO databank. LAHMA displays struc

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14

Nishiyama, A., K. J. Dahlin, J. T. Prince, S. R. Johnstone, and W. B. Stallcup. "The primary structure of NG2, a novel membrane-spanning proteoglycan." Journal of Cell Biology 114, no. 2 (1991): 359–71. http://dx.doi.org/10.1083/jcb.114.2.359.

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The complete primary structure of the core protein of rat NG2, a large, chondroitin sulfate proteoglycan expressed on O2A progenitor cells, has been determined from cDNA clones. These cDNAs hybridize to an mRNA species of 8.9 kbp from rat neural cell lines. The total contiguous cDNA spans 8,071 nucleotides and contains an open reading frame for 2,325 amino acids. The predicted protein is an integral membrane protein with a large extracellular domain (2,224 amino acids), a single transmembrane domain (25 amino acids), and a short cytoplasmic tail (76 amino acids). Based on the deduced amino aci

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15

Vallat, Philippe, Patrick Gaillard, Pierre-Alain Carrupt, Ruey-Shiuan Tsai, and Bernard Testa. "Structure-Lipophilicity and Structure-Polarity relationships of amino acids and peptides." Helvetica Chimica Acta 78, no. 2 (1995): 471–85. http://dx.doi.org/10.1002/hlca.19950780218.

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16

Chen, Ray-Ming. "Distance matrices for nitrogenous bases and amino acids of SARS-CoV-2 via structural metric." Journal of Bioinformatics and Computational Biology 19, no. 04 (2021): 2150011. http://dx.doi.org/10.1142/s0219720021500116.

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COVID-19 pandemic has caused a global health crisis. Developing vaccines would need a good knowledge of genetic properties of SARS-CoV-2. The most fundamental approach is to look into the structures of its RNA, in particular, the nucleotides and amino acids. This motivates our research on this topic. We study the occurrence structures of nitrogenous bases and amino acids. To this aim, we devise a structural metric which could measure the structure differences for bases or amino acids. By analyzing various SARS-CoV-2 samples, we calculate the distance matrices for nitrogenous bases and amino ac

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17

Xu and Chung. "Quantitative Structure–Activity Relationship Study of Bitter Di-, Tri- and Tetrapeptides Using Integrated Descriptors." Molecules 24, no. 15 (2019): 2846. http://dx.doi.org/10.3390/molecules24152846.

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New quantitative structure–activity relationship (QSAR) models for bitter peptides were built with integrated amino acid descriptors. Datasets contained 48 dipeptides, 52 tripeptides and 23 tetrapeptides with their reported bitter taste thresholds. Independent variables consisted of 14 amino acid descriptor sets. A bootstrapping soft shrinkage approach was utilized for variable selection. The importance of a variable was evaluated by both variable selecting frequency and standardized regression coefficient. Results indicated model qualities for di-, tri- and tetrapeptides with R2 and Q2 at 0.9

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18

V. Okunev, Rodion, Elena S. Vaganova, and . "Laboratory Research of the Effect Fertilizers on the Soil Structure." International Journal of Engineering & Technology 7, no. 4.7 (2018): 212. http://dx.doi.org/10.14419/ijet.v7i4.7.20547.

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Phosphorus is an important element of plant nutrition, affecting the biotransformation of nitrogen in soils. The effect of the application of phosphorus fertilizers on the mineralization of nitrogen in soils is actively studied, however, little attention is paid to their effect on the content of intermediate mineralization compounds, such as free amino acids. This study evaluated the effect of various doses of ground phosphate flour and simple superphosphate (0; 1.0, 2.1, 4.2, 10.6, 53.1, 212.5, 1062.5 g kg-1) in the incubation experiment on the content of 15 free amino acids in the soil. At v

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19

Kondratyev, Sergey. "CHOICE OF MOLECULE STRUCTURE AND COMPOSITION BASED ON WORKING MECHANIZM OF PHYSICALLY SORBED COLLECTROR’S FORM." Interexpo GEO-Siberia 2, no. 4 (2019): 61–68. http://dx.doi.org/10.33764/2618-981x-2019-2-4-61-68.

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In the paper choice method of collector’s molecule structure and composition is shown based on dependence of collecting activity of floatation reagent on power of surface flow of its physically sorbed forms. The method allows to discover influence of structure and composition specialties hydrocarbon fragment and molecule of floatation reagent-collector on extraction of useful component and quality of concentrate. Particular methods of conscious choice of structure and composition of hydrocarbon fragment of collector’s molecule in the context of some known collectors such as N-acidified amino a

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20

Elliott, S., T. Lorenzini, D. Chang, et al. "Fine-structure epitope mapping of antierythropoietin monoclonal antibodies reveals a model of recombinant human erythropoietin structure." Blood 87, no. 7 (1996): 2702–13. http://dx.doi.org/10.1182/blood.v87.7.2702.bloodjournal8772702.

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We have isolated and mapped the rHuEPO epitopes for three noncompeting anti-EPO monoclonal antibodies (MoAbs). The MoAb 9G8A recognizes a linear epitope that includes amino acids 13, 16, and 17. MoAb F12 recognizes a conformational epitope that includes amino acids 31 through 33, 86 through 91, and 138. MoAb D11 recognizes a conformational epitope that includes amino acids 64 through 78 and 99 through 110. MoAb D11 neutralizes rHuEPO activity which suggests that its epitope may contain the receptor binding domain. Analysis of the effect of mutations on folding allowed the identification of bur

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21

Fábián, László, James A. Chisholm, Peter T. A. Galek, W. D. Samuel Motherwell, and Neil Feeder. "Hydrogen-bond motifs in the crystals of hydrophobic amino acids." Acta Crystallographica Section B Structural Science 64, no. 4 (2008): 504–14. http://dx.doi.org/10.1107/s0108768108019149.

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A computer program has been developed to survey a set of crystal structures for hydrogen-bond motifs. Possible ring and chain motifs are generated automatically from a user-defined list of interacting molecular fragments and intermolecular interactions. The new program was used to analyse the hydrogen-bond networks in the crystals of 52 zwitterionic α-amino acids. All the possible chain motifs (repeating 1–4 molecules) are frequent, while the frequency of ring motifs (2–6 molecules) ranges from 0 to 85% of the structures. The list of motifs displayed by each structure reveals structural simila

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22

ZHENG, WEI-MOU. "CLUSTERING OF AMINO ACIDS FOR PROTEIN SECONDARY STRUCTURE PREDICTION." Journal of Bioinformatics and Computational Biology 02, no. 02 (2004): 333–42. http://dx.doi.org/10.1142/s0219720004000582.

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Simple hidden Markov models are proposed for predicting secondary structure of a protein from its amino acid sequence. Since the length of protein conformation segments varies in a narrow range, we ignore the duration effect of length distribution, and focus on inclusion of short range correlations of residues and of conformation states in the models. Conformation-independent and -dependent amino acid coarse-graining schemes are designed for the models by means of proper mutual information. We compare models of different level of complexity, and establish a practical model with a high predicti

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23

Seebacher, U., and M. Ramek. "Structure-energy relationship in?-amino acids and related compounds." Amino Acids 7, no. 2 (1994): 223–30. http://dx.doi.org/10.1007/bf00814162.

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24

König, Burkhard, and Christoph Bonauer. "Synthesis and Structure of Chiral Methoxypyrrole Amino Acids (MOPAS)." Synthesis, no. 14 (2005): 2367–72. http://dx.doi.org/10.1055/s-2005-870023.

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25

Lewiński, Janusz, Iwona Justyniak, Janusz Zachara, and Ewa Tratkiewicz. "Structure and Reactivity of Organoaluminum Derivatives of Amino Acids." Organometallics 22, no. 20 (2003): 4151–57. http://dx.doi.org/10.1021/om030484i.

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26

TSAI, R. S., B. TESTA, N. EL TAYAR, and P. A. CARRUPT. "ChemInform Abstract: Structure-Lipophilicity Relationships of Zwitterionic Amino Acids." ChemInform 23, no. 6 (2010): no. http://dx.doi.org/10.1002/chin.199206263.

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27

Andreoli, R., A. Barbieri, L. Benedetti, C. Fontanesi, and G. Battistuzzi Gavioli. "Molecular structure-interfacial activity relationship ofN-substituted amino acids." Journal of Electroanalytical Chemistry and Interfacial Electrochemistry 251, no. 1 (1988): 201–15. http://dx.doi.org/10.1016/0022-0728(88)80397-8.

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28

Pogliani, L. "Structure property relationships of amino acids and some dipeptides." Amino Acids 6, no. 2 (1994): 141–53. http://dx.doi.org/10.1007/bf00805842.

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29

Malkov, Saša N., Miodrag V. Živković, Miloš V. Beljanski, Michael B. Hall, and Snežana D. Zarić. "A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure." Journal of Molecular Modeling 14, no. 8 (2008): 769–75. http://dx.doi.org/10.1007/s00894-008-0313-0.

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30

KUSUDA, Kazuyuki, Takayasu KOBAYASHI, Shoko IKEDA та ін. "Mutational analysis of the domain structure of mouse protein phosphatase 2Cβ". Biochemical Journal 332, № 1 (1998): 243–50. http://dx.doi.org/10.1042/bj3320243.

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The structures of five distinct isoforms of mammalian protein phosphatase 2Cβ (PP2Cβ-1, -2, -3, -4 and -5) have previously been found to differ only at their C-terminal regions. In the present study, we performed mutational analysis of recombinant mouse PP2Cβ-1 to determine the functional domains of the molecule and elucidate the biochemical significance of the structural differences in the isoforms. Differences in affinity for [32P]phosphohistone but not for [32P]phosphocasein were observed among the five PP2Cβ isoforms. Deletion of 12 amino acids from the C-terminal end, which form a unique

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31

Uyaver, Sahin, Helen W. Hernandez, and M. Gokhan Habiboglu. "Self-assembly of aromatic amino acids: a molecular dynamics study." Physical Chemistry Chemical Physics 20, no. 48 (2018): 30525–36. http://dx.doi.org/10.1039/c8cp06239k.

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32

JOHNSON, LOUISE N. "Asymmetry at the molecular level in biology." European Review 13, S2 (2005): 77–95. http://dx.doi.org/10.1017/s1062798705000670.

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Naturally occurring biological molecules are made of homochiral building blocks. Proteins are composed of L-amino acids (and not D-amino acids); nucleic acids such as DNA have D-ribose sugars (and not L-ribose sugars). It is not clear why nature selected a particular chirality. Selection could have occurred by chance or as a consequence of basic physical chemistry. Possible proposals, including the contribution of the parity violating the weak nuclear force, are discussed together with the mechanisms by which this very small contribution might be amplified. Homochirality of the amino acids has

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33

Ou, Yu Heng, Len Chang, and Chia Ming Chang. "A Quantitative Structure-Property Relationship Study of the Adsorption of Amino Acids on Kaolinite Surfaces." International Journal of Quantitative Structure-Property Relationships 3, no. 2 (2018): 21–35. http://dx.doi.org/10.4018/ijqspr.2018070102.

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This article describes how the adsorption behaviors of various kinds of amino acids onto kaolinite surfaces were investigated by the quantum-chemical calculations and the quantitative structure-property relationships (QSPR). The QSPR results revealed that both adsorption energies of amino acids on tetrahedral Si-O and octahedral Al-O surfaces were mainly affected by the chemical potential and the negative of maximum negative charges of amino acids, which represent the electron flow and the hydrogen bonding between adsorbent-adsorbate interactions. The dispersion and polarization play a minor r

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34

Giorda, R., and H. L. Ennis. "Structure of two developmentally regulated Dictyostelium discoideum ubiquitin genes." Molecular and Cellular Biology 7, no. 6 (1987): 2097–103. http://dx.doi.org/10.1128/mcb.7.6.2097.

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A previously isolated cDNA clone, pLK229, that is specific for mRNA developmentally expressed during Dictyostelium discoideum spore germination and multicellular development, was used to screen two genomic libraries. Two genomic sequences homologous to pLK229 were isolated and sequenced. Genomic clone p229 is identical to the cDNA clone pLK229 and codes for a polypeptide of 381 amino acids. This polypeptide is composed of five tandem repeats of the same 76-amino-acid sequence. Clone lambda 229 codes for a protein of 229 amino acids, containing three tandem repeats of the identical 76-amino-aci

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Giorda, R., and H. L. Ennis. "Structure of two developmentally regulated Dictyostelium discoideum ubiquitin genes." Molecular and Cellular Biology 7, no. 6 (1987): 2097–103. http://dx.doi.org/10.1128/mcb.7.6.2097-2103.1987.

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A previously isolated cDNA clone, pLK229, that is specific for mRNA developmentally expressed during Dictyostelium discoideum spore germination and multicellular development, was used to screen two genomic libraries. Two genomic sequences homologous to pLK229 were isolated and sequenced. Genomic clone p229 is identical to the cDNA clone pLK229 and codes for a polypeptide of 381 amino acids. This polypeptide is composed of five tandem repeats of the same 76-amino-acid sequence. Clone lambda 229 codes for a protein of 229 amino acids, containing three tandem repeats of the identical 76-amino-aci

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36

Stankova, Ivanka, Radoslav Chayrov, Michaela Schmidtke, et al. "Quantitative structure-activity relationship modelling of influenza M2 ion channels inhibitors." Journal of the Serbian Chemical Society 86, no. 7-8 (2021): 625–37. http://dx.doi.org/10.2298/jsc200509036s.

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A series of adamantane derivatives (rimantadine and amantadine) incorporating amino-acid residues are investigated by simplex representation of molecular structure (SiRMS) approach in order to found correlation between chemical structures of investigated compounds and obtained data for antiviral activity and cytotoxicity. The obtained data from QSAR analysis show that adamantane derivatives containing amino acids with short aliphatic non-polar residues in the lateral chain will have good antiviral activity against the tested virus A/H3N2, strain Hong Kong/68 with low cytotoxicity. QSAR experim

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37

Ichinose, Mitsuyuki, and D. J. McAdoo. "Excitatory effect of amino acids on identified neuron R14 ofAplysia. II. Neutral amino acids and structure-activity relationships." Journal of Neuroscience Research 14, no. 1 (1985): 145–58. http://dx.doi.org/10.1002/jnr.490140113.

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38

Ghalib, Mohammed, Joanna Lach, Olga S. Fomina, Dmitry G. Yakhvarov, Peter G. Jones, and Joachim Heinicke. "Benzazaphospholine-2-carboxylic acids: Synthesis, structure and properties of heterocyclic phosphanyl amino acids." Polyhedron 77 (July 2014): 10–16. http://dx.doi.org/10.1016/j.poly.2014.03.046.

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39

Skolnick, Jeffrey, Hongyi Zhou, and Mu Gao. "On the possible origin of protein homochirality, structure, and biochemical function." Proceedings of the National Academy of Sciences 116, no. 52 (2019): 26571–79. http://dx.doi.org/10.1073/pnas.1908241116.

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Living systems have chiral molecules, e.g., native proteins that almost entirely contain L-amino acids. How protein homochirality emerged from a background of equal numbers of L and D amino acids is among many questions about life’s origin. The origin of homochirality and its implications are explored in computer simulations examining the stability and structural and functional properties of an artificial library of compact proteins containing 1:1 (termed demi-chiral), 3:1, and 1:3 ratios of D:L and purely L or D amino acids generated without functional selection. Demi-chiral proteins have sho

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40

Yokoi, Hidenori, and Takatoshi Kinoshita. "Strategy for Designing Self-Assembling Peptides to Prepare Transparent Nanofiber Hydrogel at Neutral pH." Journal of Nanomaterials 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/537262.

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This study examined the formation of nanofiber hydrogels at neutral pH for 16 types of peptides with different net charges, hydrophobicities, and degrees of polymerization. The peptides formed various hydrogels depending on the arrangement of charged amino acids in the antiparallelβ-sheet structure. Circular dichroism (CD) measurement, atomic force microscopy (AFM), visible light spectroscopy, and dynamic viscoelasticity measurement showed that the formation of transparent nanofiber hydrogels in peptides requires at least 2 additional positively or negatively charged amino acids per peptide. W

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Vojisavljevic, V., E. Pirogova, D. M. Davidovic та I. Cosic. "Hybrid approach to analysis of β-sheet structures based on signal processing and statistical consideration". Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 467, № 2128 (2010): 1052–72. http://dx.doi.org/10.1098/rspa.2010.0382.

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A number of biotechnology applications are based on protein design. For this design, the relationship between a protein’s primary structure and its conformation is of vital importance. A β-sheet is a common feature of a protein’s two-dimensional structure; therefore, elucidating the principles governing β-sheet structure and its stability is critical for understanding the protein-folding process. In the three-dimensional representation of protein molecules, C α carbon coordinates (carbon atom immediately adjacent to the carboxylate group) have often been employed instead of the complete set of

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Baratova, Ludmila A., Aleksander V. Efimov, Eugenie N. Dobrov, et al. "In Situ Spatial Organization of Potato Virus A Coat Protein Subunits as Assessed by Tritium Bombardment." Journal of Virology 75, no. 20 (2001): 9696–702. http://dx.doi.org/10.1128/jvi.75.20.9696-9702.2001.

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ABSTRACT Potato virus A (PVA) particles were bombarded with thermally activated tritium atoms, and the intramolecular distribution of the label in the amino acids of the coat protein was determined to assess their in situ steric accessibility. This method revealed that the N-terminal 15 amino acids of the PVA coat protein and a region comprising amino acids 27 to 50 are the most accessible at the particle surface to labeling with tritium atoms. A model of the spatial arrangement of the PVA coat protein polypeptide chain within the virus particle was derived from the experimental data obtained

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Laco, Gary S., and Yves Pommier. "Role of a tryptophan anchor in human topoisomerase I structure, function and inhibition." Biochemical Journal 411, no. 3 (2008): 523–30. http://dx.doi.org/10.1042/bj20071436.

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Human Top1 (topoisomerase I) relaxes supercoiled DNA during cell division and transcription. Top1 is composed of 765 amino acids and contains an unstructured N-terminal domain of 200 amino acids, and a structured functional domain of 565 amino acids that binds and relaxes supercoiled DNA. In the present study we examined the region spanning the junction of the N-terminal domain and functional domain (junction region). Analysis of several published Top1 structures revealed that three tryptophan residues formed a network of aromatic stacking interactions and electrostatic interactions that ancho

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Ferri-Fioni, Maria-Laura, Emmanuelle Schmitt, Julie Soutourina, Pierre Plateau, Yves Mechulam, and Sylvain Blanquet. "Structure of Crystallined-Tyr-tRNATyrDeacylase." Journal of Biological Chemistry 276, no. 50 (2001): 47285–90. http://dx.doi.org/10.1074/jbc.m106550200.

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Cell growth inhibition by severald-amino acids can be explained by anin vivoproduction ofd-aminoacyl-tRNA molecules.Escherichia coliand yeast cells express an enzyme,d-Tyr-tRNATyrdeacylase, capable of recycling suchd-aminoacyl-tRNA molecules into free tRNA andd-amino acid. Accordingly, upon inactivation of the genes of the above deacylases, the toxicity ofd-amino acids increases. Orthologs of the deacylase are found in many cells. In this study, the crystallographic structure of dimericE. colid-Tyr-tRNATyrdeacylase at 1.55 Å resolution is reported. The structure corresponds to a β-barrel close

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Balaji Munivelan. "Identification of the mutated sites present in the transmembrane regions of SCN1A_HUMAN (Sodium Voltage-Gated Channel Alpha Subunit 1) using Insilico techniques." International Journal of Pharmacometrics and Integrated Biosciences 5, no. 1 (2020): 1–6. http://dx.doi.org/10.26452/ijpib.v5i1.1149.

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Mutations in numerous genes which encode for voltage-gated sodium channels give rise to various epilepsy syndromes in humans. Our research investigation mainly focuses on the identification of the integral membrane protein of the SCN1A (Sodium Voltage-Gated Channel Alpha Subunit 1) in humans. Secondary, we focus on the transmembrane membrane (TP) amino acids directly involved in the epilepsy-involved mutated regions. Using Insilico protocols, we identify the TP proteins and amino acids and elucidate the Transmembrane Helix and the inside and outside amino acids regions of the SCN1A. With the h

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Arkhipov, Sergey G., Evgeniy A. Losev, and Elena V. Boldyreva. "New 1:1 and 2:1 salts in the `DL-norvaline–maleic acid' system as an example of assembling various crystal structures from similar supramolecular building blocks." Acta Crystallographica Section C Structural Chemistry 73, no. 1 (2017): 13–19. http://dx.doi.org/10.1107/s2053229616018271.

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Molecular salts and cocrystals of amino acids have potential applications as molecular materials with nonlinear optical, ferroelectric, piezoelectric, and other various target physical properties. The wide choice of amino acids and coformers makes it possible to design various crystal structures. The amino acid–maleic acid system provides a perfect example of a rich variety of crystal structures with different stoichiometries, symmetries and packing motifs built from the molecular building blocks, which are either exactly the same, or differ merely by protonation or as optical isomers. The pre

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Wootton, Sarah, Gabriella Koljesar, Liuzhan Yang, Kyoung-Jin Yoon, and Dongwan Yoo. "Antigenic Importance of the Carboxy-Terminal Beta-Strand of the Porcine Reproductive and Respiratory Syndrome Virus Nucleocapsid Protein." Clinical Diagnostic Laboratory Immunology 8, no. 3 (2001): 598–603. http://dx.doi.org/10.1128/cdli.8.3.598-603.2001.

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ABSTRACT Five domains of antigenic importance were previously mapped on the nucleocapsid protein (N) of the porcine reproductive and respiratory syndrome virus (PRRSV), and a domain comprised of the 11 C-terminal-most amino acids (residues 112 to 123) was shown to be essential for binding of N-specific conformation-dependent monoclonal antibodies (MAbs). In the present study, the importance of individual residues within this C-terminal domain for antigenicity was investigated using eight different mutant constructs of N expressed in HeLa cells. Single amino acid substitutions were introduced i

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Fietz, M. J., R. B. Presland, and G. E. Rogers. "The cDNA-deduced amino acid sequence for trichohyalin, a differentiation marker in the hair follicle, contains a 23 amino acid repeat." Journal of Cell Biology 110, no. 2 (1990): 427–36. http://dx.doi.org/10.1083/jcb.110.2.427.

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Trichohyalin is a highly expressed protein within the inner root sheath of hair follicles and is similar, or identical, to a protein present in the hair medulla. In situ hybridization studies have shown that trichohyalin is a very early differentiation marker in both tissues and that in each case the trichohyalin mRNA is expressed from the same single copy gene. A partial cDNA clone for sheep trichohyalin has been isolated and represents approximately 40% of the full-length trichohyalin mRNA. The carboxy-terminal 458 amino acids of trichohyalin are encoded, and the first 429 amino acids consis

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Rudack, Till, Christian Teuber, Marvin Scherlo, et al. "The Ras dimer structure." Chemical Science 12, no. 23 (2021): 8178–89. http://dx.doi.org/10.1039/d1sc00957e.

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By combining the incorporation of unnatural amino acids, click chemistry, FRET and EPR distance measurements, protein modeling and biomolecular simulations, we obtained an unambiguous Ras dimer structural model and disrupt the dimer by mutagenesis.

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Dippel, Andrew B., Gregory M. Olenginski, Nicole Maurici, Melanie T. Liskov, Scott H. Brewer, and Christine M. Phillips-Piro. "Probing the effectiveness of spectroscopic reporter unnatural amino acids: a structural study." Acta Crystallographica Section D Structural Biology 72, no. 1 (2016): 121–30. http://dx.doi.org/10.1107/s2059798315022858.

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The X-ray crystal structures of superfolder green fluorescent protein (sfGFP) containing the spectroscopic reporter unnatural amino acids (UAAs) 4-cyano-L-phenylalanine (pCNF) or 4-ethynyl-L-phenylalanine (pCCF) at two unique sites in the protein have been determined. These UAAs were genetically incorporated into sfGFP in a solvent-exposed loop region and/or a partially buried site on the β-barrel of the protein. The crystal structures containing the UAAs at these two sites permit the structural implications of UAA incorporation for the native protein structure to be assessed with high resolut

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