The Experts below are selected from a list of 294 Experts worldwide ranked by ideXlab platform
Hui Zhu - One of the best experts on this subject based on the ideXlab platform.
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Unambiguous assignment of vibrational spectra of cyclosporins A and H.
The journal of physical chemistry. A, 2010Co-Authors: Hui Zhu, Volkhard MayAbstract:Vibrational infrared and circular dichroism spectra of two cyclosporins A and H are predicted by density functional theory calculations using the nuclear magnetic resonance proposed structure in chloroform. Spectral signatures in the important amide II, I, and A regions are identified for typical peptide secondary structures including type II' beta-Turn, antiparallel beta-sheet, inverse Gamma-Turn, N-methylated peptide bond, and side-chain H-bond. Our theoretical spectra agree very well with available experimental data in nonpolar media and unambiguously clarify their controversial vibrational assignment. The new insights into the spectral signatures of secondary structures can be very useful for peptide conformation analysis in general.
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conformations and vibrational spectra of a model tripeptide change of secondary structure upon micro solvation
Physical Chemistry Chemical Physics, 2010Co-Authors: Hui Zhu, Martine N Blom, Isabel Compagnon, Anouk M Rijs, Santanu Roy, Gert Von Helden, Burkhard SchmidtAbstract:Mid-infrared (IR) hole burning spectra of the model tripeptide Z-Aib-Pro-NHMe (Z = benzyloxycarbonyl) in gas phase and its micro-clusters with one and two methanol molecules are presented. To establish a relation between experimental spectra and the underlying conformations, calculations at the DFT [B3LYP/6-311++G(d,p)] level of theory are performed. In particular, the intra-peptide and the peptide-methanol hydrogen bonds can be identified from spectral shifts in the amide I, II, and III regions. While the unsolvated tripeptide as well as its one-methanol cluster prefer a Gamma-Turn structure, a beta-Turn structure is found for the two-methanol cluster, in agreement with previous condensed phase studies. Comparison of measured and simulated spectra reveals that the favorable methanol binding sites are at the head and tail parts of the tripeptide. The interconversions between Gamma-Turn and beta-Turn structures are governed by potential barriers below 10 kJ mol(-1) inside one of the low energy basins of the potential energy surface.
Yi Shang - One of the best experts on this subject based on the ideXlab platform.
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Improving Protein Gamma-Turn Prediction Using Inception Capsule Networks
Scientific Reports, 2018Co-Authors: Chao Fang, Yi ShangAbstract:Protein Gamma-Turn prediction is useful in protein function studies and experimental design. Several methods for Gamma-Turn prediction have been developed, but the results were unsatisfactory with Matthew correlation coefficients (MCC) around 0.2–0.4. Hence, it is worthwhile exploring new methods for the prediction. A cutting-edge deep neural network, named Capsule Network (CapsuleNet), provides a new opportunity for Gamma-Turn prediction. Even when the number of input samples is relatively small, the capsules from CapsuleNet are effective to extract high-level features for classification tasks. Here, we propose a deep inception capsule network for Gamma-Turn prediction. Its performance on the Gamma-Turn benchmark GT320 achieved an MCC of 0.45, which significantly outperformed the previous best method with an MCC of 0.38. This is the first Gamma-Turn prediction method utilizing deep neural networks. Also, to our knowledge, it is the first published bioinformatics application utilizing capsule network, which will provide a useful example for the community. Executable and source code can be download at http://dslsrv8.cs.missouri.edu/~cf797/MUFoldGammaTurn/download.html.
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Improving Protein Gamma-Turn Prediction Using Inception Capsule Networks
arXiv: Quantitative Methods, 2018Co-Authors: Chao Fang, Yi ShangAbstract:Protein Gamma-Turn prediction is useful in protein function studies and experimental design. Several methods for Gamma-Turn prediction have been developed, but the results were unsatisfactory with Matthew correlation coefficients (MCC) around 0.2-0.4. One reason for the low prediction accuracy is the limited capacity of the methods; in particular, the traditional machine-learning methods like SVM may not extract high-level features well to distinguish between Turn or non-Turn. Hence, it is worthwhile exploring new machine-learning methods for the prediction. A cutting-edge deep neural network, named Capsule Network (CapsuleNet), provides a new opportunity for Gamma-Turn prediction. Even when the number of input samples is relatively small, the capsules from CapsuleNet are very effective to extract high-level features for classification tasks. Here, we propose a deep inception capsule network for Gamma-Turn prediction. Its performance on the Gamma-Turn benchmark GT320 achieved an MCC of 0.45, which significantly outperformed the previous best method with an MCC of 0.38. This is the first Gamma-Turn prediction method utilizing deep neural networks. Also, to our knowledge, it is the first published bioinformatics application utilizing capsule network, which will provides a useful example for the community.
B. Roques - One of the best experts on this subject based on the ideXlab platform.
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NMR structure of the HIV-1 regulatory protein Vpr in H2O/trifluoroethanol. Comparison with the Vpr N-terminal (1-51) and C-terminal (52-96) domains.
European Journal of Biochemistry, 2002Co-Authors: B Wecker, N. Morellet, B Bouaziz, B. RoquesAbstract:The human immunodeficiency virus type 1, HIV-1, genome encodes a highly conserved regulatory gene product, Vpr (96 amino acids), which is incorporated into virions in quantities equivalent to those of the viral Gag protein. In infected cells, Vpr is believed to function during the early stages of HIV-1 replication (such as transcription of the proviral genome and migration of preintegration nuclear complex), blocks cells in G2 phase and triggers apoptosis. Vpr also plays a critical role in long-term AIDS disease by inducing viral infection in nondividing cells such as monocytes and macrophages. To gain deeper insight of the structure-function relationship of Vpr, the intact protein (residues 1-96) was synthesized. Its three-dimensional structure was analysed using circular dichroism and two-dimensional 1H- and 15N-NMR and refined by restrained molecular dynamics. In addition, 15N relaxation parameters (T1, T2) and heteronuclear 1H-15N NOEs were measured. The structure of the protein is characterized by a well-defined Gamma Turn(14-16)-alpha helix(17-33)-Turn(34-36), followed by a alpha helix(40-48)-loop(49-54)-alpha helix(55-83) domain and ends with a very flexible C-terminal sequence. This structural determination of the whole intact Vpr molecule provide insights into the biological role played by this protein during the virus life cycle, as such amphipathic helices are believed to be involved in protein-lipid bilayers, protein-protein and/or protein-nucleic acid interactions.
Piero A. Temussi - One of the best experts on this subject based on the ideXlab platform.
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Solution conformation of tuftsin.
Biochemistry, 1992Co-Authors: Anna Maria D'ursi, Monica Pegna, Pietro Amodeo, Henriette Molinari, Antonio Verdini, Lucia Zetta, Piero A. TemussiAbstract:Tuftsin, a natural linear tetrapeptide (Thr-Lys-Pro-Arg) of potential antitumor activity, has been studied in DMSO-d6 solution by 2D NMR spectroscopy. 1H and 13C spectra show the presence of two families of conformations characterized by a trans or cis Lys-Pro bond, respectively. The family of conformers containing the cis peptide bond is a mixture of extended structures as expected for a short linear peptide. On the contrary, the trans isomer appears to be a rigid, folded conformer, as indicated by crucial NOEs and by the exceptionally low temperature coefficient of Arg NH. Analysis of the solution data by means of energy calculations leads to a unique structure, characterized by a Lys-Pro inverse Gamma-Turn.
Susanna Lindman - One of the best experts on this subject based on the ideXlab platform.
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Comparison of three γ-Turn mimetic scaffolds incorporated into angiotensin II
Bioorganic & medicinal chemistry, 2000Co-Authors: Susanna Lindman, Gunnar Lindeberg, Fred Nyberg, Anders Karlén, Anders HallbergAbstract:Rigidification of peptides by cyclization and iterative incorporation of well-defined secondary structure mimetics constitutes one approach to the design of non-peptidergic structures with better defined conformations. We herein present the synthesis of a potential Gamma-Turn mimetic scaffold, and its incorporation in the 3-5 position of angiotensin II. Two analogues of angiotensin II (Ang II) incorporating this 1,3,5-trisubstituted benzene Gamma-Turn scaffold were synthesized. Evaluation of the compounds in a radioligand binding assay showed that they lacked affinity to the AT1 receptor. To rationalize these results a geometrical and electrostatical comparison with Ang II analogues encompassing a bicyclic scaffold that delivered inactive pseudo peptides and an azepine scaffold producing highly active ligands was made. This analysis did not provide a clear rationale for the inactivity of the benzene Gamma-Turn scaffolds.
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Design, Synthesis, and Biological Activities of Four Angiotensin II Receptor Ligands with γ-Turn Mimetics Replacing Amino Acid Residues 3−5
Journal of medicinal chemistry, 1997Co-Authors: Boris Schmidt, Susanna Lindman, Gunnar Lindeberg, Weimin Tong, Adolf Gogoll, Zhennan Lai, Madeleine Thörnwall, Barbro Synnergren, Annika Goos Nilsson, Christopher J. WelchAbstract:Disulfide cyclization is a powerful method for reducing the conformational space of a peptide. This in Turn may enable the study of its bioactive conformation. Several analogues of angiotensin II (Ang II) containing a disulfide bridge between amino acids 3 and 5 have been reported. Among these the cyclic octapeptides c[Hcy3,5]-Ang II, c[Cys3,5]-Ang II, and c[Pen 3,5]-Ang II showed significant activity at Ang II receptors. We have performed conformational analysis studies using theoretical calculations and 1H-NMR spectroscopy on tripeptide model compounds of these cyclic octapeptides which show that the cyclic moieties of c[Cys3,5]-Ang II and c[Pen3,5]-Ang II preferentially assume an inverse Gamma-Turn conformation. On the basis of these results, we substituted amino acid residues 3-5 in Ang II with two different Gamma-Turn mimetics giving four diastereomeric Ang II analogues. Interestingly, two of these are equipotent to Ang II in binding to AT1 receptors. In the contractile test using rabbit aorta rings, one of the analogues is an agonist with full contractile activity approximately equipotent to c[Pen3,5]-Ang II but 300-fold less potent than Ang II. This low potency may suggest that Ang II does not adopt a Gamma-Turn in the 3-5 region when interacting with the receptor.
