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https://www.readbyqxmd.com/read/30020551/evolutionary-couplings-and-sequence-variation-effect-predict-protein-binding-sites
#1
Maria Schelling, Thomas A Hopf, Burkhard Rost
Binding small ligands such as ions or macromolecules such as DNA, RNA and other proteins is one important aspect of the molecular function of proteins. Many binding sites remain without experimental annotations. Predicting binding sites on a per-residue level is challenging, but if 3D structures are known, information about coevolving residue pairs (evolutionary couplings) can predict catalytic residues through mutual information. Here, we predicted protein binding sites from evolutionary couplings derived from a global statistical model using maximum entropy...
July 18, 2018: Proteins
https://www.readbyqxmd.com/read/30019778/singular-value-decomposition-for-the-correlation-of-atomic-fluctuations-with-arbitrary-angle
#2
Miao Yu, Xiaomin Ma, Huaiqing Cao, Bin Chong, Luhua Lai, Zhirong Liu
Many proteins exhibit a critical property called allostery, which enables intra-molecular transmission of information between distal sites. Microscopically, allosteric response is closely related to correlated atomic fluctuations. Conventional correlation analysis correlates the atomic fluctuations at two sites by taking the dot product between the fluctuations, which accounts only for the parallel and antiparallel components. Here, we present a singular value decomposition (SVD) method that analyzes the correlation coefficient of fluctuation dynamics with an arbitrary angle between the correlated directions...
July 18, 2018: Proteins
https://www.readbyqxmd.com/read/30019777/coil-conversion-to-%C3%AE-strand-induced-by-dimerisation
#3
Johanna Laibe, Aaron Caffrey, Melanie Broutin, Solene Guiglion, Barbara Pierscionek, Jean-Christophe Nebel
Most molecular processes in living organisms rely on protein-protein interactions, many of which are mediated by β-sheet interfaces; this study investigates the formation of β-sheet interfaces through the conversion of coils into β-strands. Following an exhaustive search in the Protein Data Bank, the corresponding structural dimorphic fragments were extracted, characterised and analysed. Their short strand lengths and specific amino acid profiles indicate that dimorphic β-strand interfaces are likely to be less stable than standard ones and could even convert to coil interfaces if their environment changes...
July 18, 2018: Proteins
https://www.readbyqxmd.com/read/30019774/human-telomerase-protein-understanding-how-the-catalytic-activity-is-suppressed-under-single-substitutions-of-some-conserved-residues-a-computational-study
#4
F E Herrera, S J Sferco
The Reverse Transcriptase domain in telomerase proteins contains the essential conserved residues to catalyze the addition of a single nucleotide to the ends of DNA strands of most eukaryotic cells. In human telomerase protein, mutations in the conserved residues K902, R631, K626, D712, D868 and D869 are known to suppress catalytic activity. To understand these results, a computational model was constructed to simulate a ternary complex consisting of a model of the protein reverse transcriptase domain, a DNA/RNA double helix, an incoming dNTP, and two Mg2+ ions...
July 18, 2018: Proteins
https://www.readbyqxmd.com/read/30019773/computational-characterization-of-the-binding-mode-between-oncoprotein-ets-1-and-dna-repair-enzymes
#5
Jerome de Ruyck, Guillaume Brysbaert, Vincent Villeret, Marc Aumercier, Marc F Lensink
The Ets-1 oncoprotein is a transcription factor that promotes target gene expression in specific biological processes. Typically, Ets-1 activity is low in healthy cells, but elevated levels of expression have been found in cancerous cells, specifically related to tumor progression. Like the vast majority of the cellular effectors, Ets-1 does not act alone but in association with partners. Given the important role that is attributed to Ets-1 in major human diseases, it is crucial to identify its partners and characterize their interactions...
July 18, 2018: Proteins
https://www.readbyqxmd.com/read/30019772/monitoring-transient-events-in-ir-spectra-using-local-mode-analysis
#6
M Massarczyk, J Schlitter, C Kötting, T Rudack, K Gerwert
Time-resolved fourier transformed infrared (FTIR) spectroscopy of chemical reactions is highly sensitive to minimal spatiotemporal changes. Structural features are decoded and represented in a comprehensible manner by combining FTIR spectroscopy with biomolecular simulations. Local mode analysis (LMA) is a tool to connect molecular motion based on a quantum mechanics simulation with IR spectral features and vice versa. Here we present the python based software tool of LMA and demonstrate the novel feature of LMA to extract transient structural details and identify the related IR spectra at the case example of malonaldehyde (MA)...
July 18, 2018: Proteins
https://www.readbyqxmd.com/read/30019770/%C3%AE-strand-twisting-bending-in-soluble-and-transmembrane-%C3%AE-barrel-structures
#7
Nobuaki Kikuchi, Kazuo Fujiwara, Masamichi Ikeguchi
The majority of β-strands in globular proteins have a right-handed twist and bend. The dominant driving force for β-strand twisting is thought to be inter-strand hydrogen bonds. We previously demonstrated that, for water-soluble proteins, both the twisting and bending of β-strand are suppressed by the polar side chains of serine, threonine, and asparagine residues. To determine whether this also holds for transmembrane β-strands, we calculated and statistically analyzed the twist and bend angles of four-residue frames of β-strands in both transmembrane and water-soluble β-barrel proteins with known three-dimensional structures...
July 18, 2018: Proteins
https://www.readbyqxmd.com/read/30007053/binding-and-structural-studies-of-the-complexes-of-type-1-ribosome-inactivating-protein-from-momordica-balsamina-with-uracil-and-uridine
#8
Sada Nand Pandey, Naseer Iqbal, Prashant K Singh, Nilisha Rastogi, Punit Kaur, Sujata Sharma, Tej P Singh
Ribosome inactivating protein (RIP) catalyzes the cleavage of glycosidic bond formed between adenine and ribose sugar of ribosomal RNA to inactivate ribosomes. Previous structural studies have shown that RNA bases, adenine, guanine and cytosine tend to bind to RIP in the substrate binding site. However, the mode of binding of uracil with RIP was not yet known. Here, we report crystal structures of two complexes of type 1 RIP from Momordica balsamina (MbRIP1) with base, uracil and nucleoside, uridine. The binding studies of MbRIP1 with uracil and uridine as estimated using fluorescence spectroscopy showed that the equilibrium dissociation constants (KD ) were 1...
July 14, 2018: Proteins
https://www.readbyqxmd.com/read/30007037/refined-structure-of-bem9-reveals-arginine-hand-an-overlooked-structural-motif-in-scorpion-toxins-affecting-sodium-channels
#9
Nikita A Kuldyushev, Konstantin S Mineev, Antonina A Berkut, Steve Peigneur, Alexander S Arseniev, Jan Tytgat, Eugene V Grishin, Alexander A Vassilevski
Sodium channel alpha-toxins from scorpion venom (α-NaTx) inhibit the inactivation of voltage-gated sodium channels. We used solution NMR to investigate the structure of BeM9 toxin from Mesobuthus eupeus scorpion, a prototype α-NaTx classified as an "α-like" toxin due to its wide spectrum of activity on insect and mammalian channels. We identified a new motif that we named "arginine hand", whereby arginine side chain forms several hydrogen bonds with main chain atoms. The arginine hand was found in the "specificity module", a part of the molecule that dictates toxin selectivity; and just single arginine-to-lysine point mutation drastically changed BeM9 selectivity profile...
July 14, 2018: Proteins
https://www.readbyqxmd.com/read/29907987/mutational-analysis-of-the-pro-peptide-of-a-marine-intracellular-subtilisin-protease-supports-its-role-in-inhibition
#10
Gro E K Bjerga, Øivind Larsen, Hasan Arsın, Adele Williamson, Antonio García-Moyano, Ingar Leiros, Pål Puntervoll
Intracellular subtilisin proteases (ISPs) have important roles in protein processing during the stationary phase in bacteria. Their unregulated protein degrading activity may have adverse effects inside a cell, but little is known about their regulatory mechanism. Until now, ISPs have mostly been described from Bacillus species, with structural data from a single homolog. Here, we study a marine ISP originating from a phylogenetically distinct genus, Planococcus sp. The enzyme was successfully overexpressed in E...
June 16, 2018: Proteins
https://www.readbyqxmd.com/read/29790608/how-accurately-do-force-fields-represent-protein-side-chain-ensembles
#11
Dušan Petrović, Xue Wang, Birgit Strodel
Although the protein backbone is the most fundamental part of the structure, the fine-tuning of side-chain conformations is important for protein function, for example, in protein-protein and protein-ligand interactions, and also in enzyme catalysis. While several benchmarks testing the performance of protein force fields for side chain properties have already been published, they often considered only a few force fields and were not tested against the same experimental observables; hence, they are not directly comparable...
May 23, 2018: Proteins
https://www.readbyqxmd.com/read/29790602/folding-with-a-protein-s-native-shortcut-network
#12
Susan Khor
A complex network approach to protein folding is proposed, wherein a protein's contact map is re-conceptualized as a network of shortcut edges, and folding is steered by a structural characteristic of this network. Shortcut networks are generated by a known message passing algorithm operating on protein residue networks. It is found that the shortcut networks of native structures (SCN0s) are relevant graph objects with which to study protein folding at a formal level. The logarithm form of their contact order (SCN0_lnCO) correlates significantly with folding rate of two-state and non-two-state proteins...
May 23, 2018: Proteins
https://www.readbyqxmd.com/read/29790601/a-method-for-partitioning-the-information-contained-in-a-protein-sequence-between-its-structure-and-function
#13
Andrea Possenti, Michele Vendruscolo, Carlo Camilloni, Guido Tiana
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance between the amount of information supplied by the sequence and that left after that the protein has folded into its structure. We study the amount of information necessary to specify the protein structure, providing an estimate that keeps into account the thermodynamic properties of protein folding...
May 23, 2018: Proteins
https://www.readbyqxmd.com/read/29790597/stability-of-structurally-entangled-protein-dimers
#14
Yani Zhao, Marek Cieplak
We studied stretching, folding and thermodynamic properties of structurally entangled protein dimers. The tests for entanglement involve four-terminal pulling. We study the dynamics of such pulling and contrast it with the standard two-terminal one. The two-chain entanglement is qualitatively characterized by its entangled core, which is defined as the minimal structure that is entangled. The existence of the entangled cores is found to be affecting both the mechanical and folding properties of the proteins...
May 23, 2018: Proteins
https://www.readbyqxmd.com/read/29726048/role-of-glycans-in-cholesteryl-ester-transfer-protein-revealed-by-molecular-dynamics-simulation
#15
Dongxiao Hao, Zhiwei Yang, Teng Gao, Zhiqi Tian, Lei Zhang, Shengli Zhang
Current cholesteryl ester transfer protein (CETP) inhibitors are designed based on the unglycosylated crystal structure, and most of them have failed to cure cardiovascular disease (CVD). It is particularly important for us to investigate the glycosylation structure of CETP (CETP-G) and effect of glycans on the structure and function of CETP. Here, we used a total of 3.0-μs molecular dynamics (MD) trajectories of nascent structure of CETP (CETP-N) and CETP-G to study their structural differentiations, to shed new light on the CETP-mediated lipid exchange...
May 3, 2018: Proteins
https://www.readbyqxmd.com/read/29722065/the-structure-of-the-n-terminal-module-of-the-cell-wall-hydrolase-ripa-and-its-role-in-regulating-catalytic-activity
#16
Eva Maria Steiner, Jeppe Lyngsø, Jodie E Guy, Gleb Bourenkov, Ylva Lindqvist, Thomas R Schneider, Jan Skov Pedersen, Gunter Schneider, Robert Schnell
RipA plays a vital role during cell division of Mycobacterium tuberculosis by degrading the cell wall peptidoglycan at the septum, allowing daughter cell separation. The peptidoglycan degrading activity relies on the NlpC/P60 domain, and as it is potentially harmful when deregulated, spatial and temporal control is necessary in this process. The N-terminal domain of RipA has been proposed to play an inhibitory role blocking the C-terminal NlpC/P60 domain. Accessibility of the active site cysteine residue is however not limited by the presence of the N-terminal domain, but by the lid-module of the inter-domain linker, which is situated in the peptide binding groove of the crystal structures of the catalytic domain...
May 2, 2018: Proteins
https://www.readbyqxmd.com/read/29722060/structure-and-properties-of-ab21-a-novel-agaricus-bisporus-protein-with-structural-relation-to-bacterial-pore-forming-toxins
#17
Jan Komárek, Eva Ivanov Kavková, Josef Houser, Aneta Horáčková, Jitka Ždánská, Gabriel Demo, Michaela Wimmerová
We report the characterization of the dimeric protein AB21 from Agaricus bisporus, one of the most commonly and widely consumed mushrooms in the world. The protein shares no significant sequence similarity with any protein of known function, and it is the first characterized member of its protein family. The coding sequence of the ab21 gene was determined and the protein was expressed in E. coli in a recombinant form. We demonstrated a high thermal and pH stability of AB21 and proved the weak affinity of the protein to divalent ions of some transition metals (nickel, zinc, cadmium, and cobalt)...
May 2, 2018: Proteins
https://www.readbyqxmd.com/read/29708626/radiation-chemists-look-at-damage-in-redox-proteins-induced-by-x-rays
#18
REVIEW
Scot Wherland, Israel Pecht
The three-dimensional structure of proteins, especially as determined by X-ray crystallography, is critical to the understanding of their function. However, the X-ray exposure may lead to damage that must be recognized and understood to interpret the crystallographic results. This is especially relevant for proteins with transition metal ions that can be oxidized or reduced. The detailed study of proteins in aqueous solution by the technique of pulse radiolysis has provided a wealth of information on the production and fate of radicals that are the same as those produced by X-ray exposure...
April 30, 2018: Proteins
https://www.readbyqxmd.com/read/29696695/mimicking-a-p53-mdm2-interaction-based-on-a-stable-immunoglobulin-like-domain-scaffold
#19
Pedro Jimenez-Sandoval, Ezequiel A Madrigal-Carrillo, Hugo A Santamaría-Suárez, Daniel Maturana, Itzel Rentería-González, Claudia G Benitez-Cardoza, Alfredo Torres-Larios, Luis G Brieba
Antibodies recognize protein targets with great affinity and specificity. However, posttranslational modifications and the presence of intrinsic disulfide-bonds pose difficulties for their industrial use. The immunoglobulin fold is one of the most ubiquitous folds in nature and it is found in many proteins besides antibodies. An example of a protein family with an immunoglobulin-like fold is the Cysteine Protease Inhibitors (ICP) family I42 of the MEROPs database for protease and protease inhibitors. Members of this protein family are thermostable and do not present internal disulfide bonds...
April 26, 2018: Proteins
https://www.readbyqxmd.com/read/29575221/arginine-side-chain-stacking-with-peptide-plane-stabilizes-the-protein-helix-conformation-in-a-cooperative-way
#20
Jia Wang, Jingfei Chen, Jingwen Li, Liaoyuan An, Yefei Wang, Qingshan Huang, Lishan Yao
A combined experimental and computational study is performed for arginine side chain stacking with the protein α-helix. Theremostability measurements of Aristaless homeodomain, a helical protein, suggest that mutating the arginine residue R106, R137 or R141, which has the guanidino side chain stacking with the peptide plane, to alanine, destabilizes the protein. The R-PP stacking has an energy of ∼0.2-0.4 kcal/mol. This stacking interaction mainly comes from dispersion and electrostatics, based on MP2 calculations with the energy decomposition analysis...
June 2018: Proteins
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