The Experts below are selected from a list of 261 Experts worldwide ranked by ideXlab platform
Arthurs Tatham - One of the best experts on this subject based on the ideXlab platform.
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scanning tunneling microscopy ofawheatseedstorage protein reveals details ofanunusual Supersecondary Structure
1991Co-Authors: Mervynj Miles, Terencec Mcmaster, Peters Belton, J Michaelfield, Peterr Shewry, Arthurs Tatham, H WillsAbstract:Scanning tunneling microscopy hasbeenused todemonstrate that aspiral Structure based on-reverse turns isadopted bytherepeat sequences present inagroup ofwheat gluten proteins. This Structure issmilar tothe«spiral formed byasynthetic polypentapeptide based onarepeat sequence present inelastin. Wheatgluten andelastin arebothelasto- meric anditispossible that thespiral Structure contributes to this property. Scanning tunneling microscopy (STM)andthederivative scanning probe techniques canproduce high-resolution im- ages ofStructures attheatomic andmolecular levels. Already usedasatool insurface science (1), manyoftheproperties ofSTMhavegreat potential forthestudy ofbiopolymers. TheSTMcanoperate inairandeveninliquid toimage uncoated andunstained biomolecules deposited onacon- ducting surface. Thisallows biopolymers intheir native hydrated state tobeimaged (2-5). STMimages ofDNA have confirmed thedetails ofthehelical Structure established by x-ray diffraction, giving confidence inthis formofmicros- copy(6-10). STMcan, therefore, beusedtoimage Structures that, toourknowledge, havenotbeendescribed byother techniques. Inthepresent study STMhasbeenusedtostudy theStructure ofahighmolecular weight (HMW)subunit protein fromwheat gluten forwhich anunusual Structure has beenpredicted fromtheamino acid sequence andonthebasis ofother physicochemical studies. TheHMW subunits ofwheatgluten appear tobelargely responsible fortheelastic behavior ofdough. Analyses of genomic clones encoding several subunits haveshownthat they havesimilar Structures (11, 12). Eachprotein consists of acentral repetitive domain, varying inlength fromabout 640 to830residues, flanked byshorter nonrepetitive N (81-104 residues)- andC(42residues)-terminal domains. TheHMW subunits areclassified into twogroups onthebasis oftheir molecular weights, x-types (molecular weights intherange 83,000-88,000) andy-types (molecular weights intherange 67,000-74,000). Thecentral repetitive domains arebased on threemotifs. Hexapeptides (consensus Pro-Gly-Gln-Gly- Gln-Gln) andnonapeptides (consensus Gly-Tyr-Tyr-Pro- Thr- Ser-Pro/Leu-Gln-Gln)
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scanning tunneling microscopy of a wheat seed storage protein reveals details of an unusual Supersecondary Structure
Proceedings of the National Academy of Sciences of the United States of America, 1991Co-Authors: M J Miles, Terencec Mcmaster, Peters Belton, Peterr Shewry, H J Carr, K J Ianson, Victor J Morris, J M Field, Arthurs TathamAbstract:Scanning tunneling microscopy has been used to demonstrate that a spiral Structure based on beta-reverse turns is adopted by the repeat sequences present in a group of wheat gluten proteins. This Structure is similar to the beta-spiral formed by a synthetic polypentapeptide based on a repeat sequence present in elastin. Wheat gluten and elastin are both elastomeric and it is possible that the spiral Structure contributes to this property.
Chuanfeng Chen - One of the best experts on this subject based on the ideXlab platform.
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Artificial Supersecondary Structures based on aromatic oligoamides.
Methods of Molecular Biology, 2012Co-Authors: Haiyu Hu, Chuanfeng ChenAbstract:: With an intelligent design of the monomers, considerable effort has so far focused on the creation of aromatic oligoamide foldamers which are able to mimic the secondary Structures of biopolymers. Supersecondary Structure is a growing set of known and classifiable protein folding patterns that provides an important organizational context to this complex endeavor. In this article, we highlight the design, chemical synthesis, and structural studies of artificial Supersecondary Structures based on aromatic oligoamide foldamers in recent years.
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conformationally constrained aromatic oligoamide foldamers with Supersecondary Structure motifs
Organic and Biomolecular Chemistry, 2009Co-Authors: Haiyu Hu, Junfeng Xiang, Chuanfeng ChenAbstract:The design, synthesis, and structural studies of aromatic foldamers based on oligo(phenanthroline dicarboxamide)s that displayed Supersecondary Structure motifs have been described. Governed by a combined conformational restriction, the foldamers adopted well defined and compact 3D Structures, which have been validated by UV/Vis, NMR spectra, and X-ray crystal analysis. The results presented here would offer a useful route for the de novo design of aromatic oligoamide foldamers with distinctive structural architectures.
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a helix turn helix Supersecondary Structure based on oligo phenanthroline dicarboxamide s
Organic Letters, 2008Co-Authors: Haiyu Hu, Junfeng Xiang, Yong Yang, Chuanfeng ChenAbstract:An artificial helix−turn−helix (HTH) Supersecondary Structure based on the oligo(phenanthroline dicarboxamide)s, in which the 2,2‘-dimethoxy-1,1‘-binaphthyl-6,6‘-diamine subunit was utilized as the turn to impart a bias in the twist sense of the Supersecondary Structure, was reported. The HTH Structure has been demonstrated by UV/vis, NMR, CD spectra, and X-ray crystal analysis.
Jeffrey Skolnick - One of the best experts on this subject based on the ideXlab platform.
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De novo and inverse folding predictions of protein Structure and dynamics
Journal of Computer-Aided Molecular Design, 1993Co-Authors: Adam Godzik, Andrzej Kolinski, Jeffrey SkolnickAbstract:In the last two years, the use of simplified models has facilitated major progress in the globular protein folding problem, viz., the prediction of the three-dimensional (3D) Structure of a globular protein from its amino acid sequence. A number of groups have addressed the inverse folding problem where one examines the compatibility of a given sequence with a given (and already determined) Structure. A comparison of extant inverse protein-folding algorithms is presented, and methodologies for identifying sequences likely to adopt identical folding topologies, even when they lack sequence homology, are described. Extension to produce structural templates or fingerprints from idealized Structures is discussed, and for eight-membered β-barrel proteins, it is shown that idealized fingerprints constructed from simple topology diagrams can correctly identify sequences having the appropriate topology. Furthermore, this inverse folding algorithm is generalized to predict elements of Supersecondary Structure including β-hairpins, helical hairpins and α/β/α fragments. Then, we describe a very high coordination number lattice model that can predict the 3D Structure of a number of globular proteins de novo; i.e. using just the amino acid sequence. Applications to sequences designed by DeGrado and co-workers [Biophys. J., 61 (1992) A265] predict folding intermediates, native states and relative stabilities in accord with experiment. The methodology has also been applied to the four-helix bundle designed by Richardson and co-workers [Science, 249 (1990) 884] and a redesigned monomeric version of a naturally occurring four-helix dimer, rop. Based on comparison to the rop dimer, the simulations predict conformations with rms values of 3–4 Å from native. Furthermore, the de novo algorithms can asses the stability of the folds predicted from the inverse algorithm, while the inverse folding algorithms can assess the quality of the de novo models. Thus, the synergism of the de novo and inverse folding algorthhm approaches provides a set of complementary tools that will facilitate further progress on the protein-folding problem.
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sequence Structure matching in globular proteins application to Supersecondary and tertiary Structure determination
Proceedings of the National Academy of Sciences of the United States of America, 1992Co-Authors: Adam Godzik, Jeffrey SkolnickAbstract:Abstract A methodology designed to address the inverse globular protein-folding problem (the identification of which sequences are compatible with a given three-dimensional Structure) is described. By using a library of protein finger-prints, defined by the side chain interaction pattern, it is possible to match each Structure to its own sequence in an exhaustive data base search. It is shown that this is a permissive requirement for the validation of the methodology. To pass the more rigorous test of identifying proteins that are not close sequence homologs, but that have similar Structure, the method has been extended to include insertions and deletions in the sequence, which is compared to the fingerprint. This allows for the identification of sequences having little or no sequence homology to the fingerprint. Examples include plastocyanin/azurin/pseudoazurin, the globin family, different families of proteases and cytochromes, including cytochromes c' and b-562, actinidin/papain, and lysozyme/alpha-lactalbumin. Turning to Supersecondary Structure prediction, we find that alpha/beta/alpha fragments possess sufficient specificity to identify their own and related sequences. By threading a beta-hairpin through a sequence, it is possible to predict the location of such hairpins and turns with remarkable fidelity. Thus, the method greatly extends existing techniques for the prediction of both global structural homology and local Supersecondary Structure.
M J Miles - One of the best experts on this subject based on the ideXlab platform.
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scanning tunneling microscopy of a wheat seed storage protein reveals details of an unusual Supersecondary Structure
Proceedings of the National Academy of Sciences of the United States of America, 1991Co-Authors: M J Miles, Terencec Mcmaster, Peters Belton, Peterr Shewry, H J Carr, K J Ianson, Victor J Morris, J M Field, Arthurs TathamAbstract:Scanning tunneling microscopy has been used to demonstrate that a spiral Structure based on beta-reverse turns is adopted by the repeat sequences present in a group of wheat gluten proteins. This Structure is similar to the beta-spiral formed by a synthetic polypentapeptide based on a repeat sequence present in elastin. Wheat gluten and elastin are both elastomeric and it is possible that the spiral Structure contributes to this property.
Hiroshi Izumi - One of the best experts on this subject based on the ideXlab platform.
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spike protein undeformable motif shared by sars cov 2 and sars cov flexible conformations predicted by using deep neural network based programs of Supersecondary Structure codes
Authorea Preprints, 2020Co-Authors: Hiroshi IzumiAbstract:A deep neural network-based program for sequence-based prediction of Supersecondary Structure codes (SSSCs), called SSSCPrediction (SSSCPred) was constructed. Furthermore, to predict the flexibility and conformational change of proteins, a comparison program of three deep-neural-network-based prediction systems (SSSCPred200, SSSCPred100, and SSSCPred) was developed. I compared the predicted and observed flexible conformations of SARS-CoV-2 and SARS-CoV spike proteins by using SSSCs and the comparison program. The SARS-CoV SSSC sequences of the receptor-binding motif predicted by the three deep-neural-network-based systems well reproduced those of the Protein Data Bank (PDB) data, including the Structured loops. In contrast, the receptor-binding motif SSSCs of SARS-CoV-2 differs greatly from those of SARS-CoV, with that of SARS-CoV-2 being more flexible. Only one common identical motif (SSSC: SSSHSSHHHH) among all of the compared SSSC sequences, including predicted and observed ones, was found at the S2 subunit. This motif has an extremely rare and relatively undeformable conformation. The comparison program may be helpful to explore undeformable drug discovery targets of many unsolved protein Structures.
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homology searches using Supersecondary Structure code
Methods of Molecular Biology, 2019Co-Authors: Hiroshi IzumiAbstract:: Supersecondary Structure code (SSSC), which is represented as the combination of α-helix-type (SSSC: H), β-sheet-type (SSSC: S), the other (SSSC: T), and disorder residue or C-terminal (SSSC: D) patterns, has been produced by the developed concept of Ramachandran plot, in addition, with the ω angle and with the specification of positions of torsion angles in a protein by the registration of codes for torsion angles of each amino acid peptide unit, derived from the fuzzy search of structural code homology using the template patterns 3a5c4a (SSSC: H) and 6c4a4a (SSSC: S) with conformational codes. The DSSP (Dictionary of Secondary Structure in Proteins) method assigns the secondary Structure including hydrogen bond well. In contrast, Supersecondary Structure code is very sensitive to the Supersecondary Structures of proteins. In this chapter, the protocol of homology search methods, the sequence alignment using Supersecondary Structure code, the assignment of Supersecondary Structure code T, the fuzzy search using Supersecondary Structure code, and the exact search using Supersecondary Structure code are described. Supersecondary Structure code is variable with the conformational change. If possible, many Protein Data Bank (PDB) data of similar main chains of proteins should be used for the homology searches. The thorough check of SSSC sequences is also useful to reveal the role of target pattern.
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data mining of Supersecondary Structure homology between light chains of immunogloblins and mhc molecules absence of the common conformational fragment in the human igm rheumatoid factor
Journal of Chemical Information and Modeling, 2013Co-Authors: Hiroshi Izumi, Wakisaka Akihiro, Laurence A Nafie, Rina K DukorAbstract:It is shown that fuzzy search and data mining techniques of Supersecondary Structure homology for subunits of proteins using conformational code patterns of α-helix-type (3β5α4β) and β-sheet-type (6α4β4β) fragments can be used to extract correlations between fragments of MHC class I molecules and the light chain of immunoglobulins. The new method of conformational pattern analysis with fuzzy search of structural code homology reflects well the shape of main chain rather than secondary Structure in comparison with the DSSP method. Further, the data mining technique using the combination of h- and s-fragment patterns can quantify the Supersecondary Structure homology between any subunits of proteins with different amino acid sequences. Characteristic fragment patterns (string “shhshss”), which were sandwiched between two identical amino acid sequences His and Pro, were found in light chains of various types of immunogloblins, α-chain and β-2 microglobulin of MHC class I and α-chain and β-chain of MHC class ...