Backbone Movement Research Articles

Characterization and Molecular Dynamics Simulation of a Lipase Capable of Improving the Functional Characteristics of an Egg-Yolk-Contaminated Liquid Egg White.

Lipase has great application potential in hydrolyzing residual yolk lipid in egg white liquid to restore its functional properties. In this study, a lipase gene from Bacillus subtilis was expressed in E. coli BL21 (DE3) and named Lip-IM. Results showed that although Lip-IM has stronger specificity for medium- and short-chain substrates than long-chain substrates (C16, C18), due to its excellent enzyme activity, it also has strong hydrolysis activity for long-chain substrates and maintained over 80% activity at 4-20 °C, but significantly reduced when the temperature exceeds 40 °C. The addition of 0.5% Lip-IM enhanced foaming ability by 26% (from 475 to 501%) and reduced liquid precipitation rate by 9% (from 57 to 48%). Furthermore, molecular dynamics (MD) simulations were run to investigate the conformational stability of Lip-IM at different temperatures. Results showed that Lip-IM maintained a stable conformation within the temperature range of 277-303 K. Fluctuations in the flexible area and backbone movement of proteins were identified as the main reasons for its poor thermal stability.

A Study of a Protein-Folding Machine: Transient Rotation of the Polypeptide Backbone Facilitates Rapid Folding of Protein Domains in All-Atom Molecular Dynamics Simulations.

Molecular dynamics simulations of protein folding typically consider the polypeptide chain at equilibrium and in isolation from the cellular components. We argue that in order to understand protein folding as it occurs in vivo, it should be modeled as an active, energy-dependent process, in which the cellular protein-folding machine directly manipulates the polypeptide. We conducted all-atom molecular dynamics simulations of four protein domains, whose folding from the extended state was augmented by the application of rotational force to the C-terminal amino acid, while the movement of the N-terminal amino acid was restrained. We have shown earlier that such a simple manipulation of peptide backbone facilitated the formation of native structures in diverse α-helical peptides. In this study, the simulation protocol was modified, to apply the backbone rotation and movement restriction only for a short time at the start of simulation. This transient application of a mechanical force to the peptide is sufficient to accelerate, by at least an order of magnitude, the folding of four protein domains from different structural classes to their native or native-like conformations. Our in silico experiments show that a compact stable fold may be attained more readily when the motions of the polypeptide are biased by external forces and constraints.

An online GPCR structure analysis platform.

We present an online, interactive platform for comparative analysis of all available G-protein coupled receptor (GPCR) structures while correlating to functional data. The comprehensive platform encompasses structure similarity, secondary structure, protein backbone packing and movement, residue-residue contact networks, amino acid properties and prospective design of experimental mutagenesis studies. This lets any researcher tap the potential of sophisticated structural analyses enabling a plethora of basic and applied receptor research studies.

An investigation of NMR‐Derived Structures for the SARS Coronavirus E Channel Protein

During the current Covid‐19 pandemic, college laboratories are shut down and undergraduate students who need research experience are having a hard time gaining those skills. Against this backdrop we developed a pilot project that would introduce students to internationally available online biochemical databases, open‐source modeling software and animation tools. The students received individual hands‐on training to generate data allowing them to engage in discovery and contextualize learning as they would in a face‐to face laboratory setting. We describe an investigation of NMR‐based structures of a SARS coronavirus E channel protein, structures found in the 5X29 pdb file deposited by Surya, Li, &, Torres, and described in (2018) Biochim. Biophys. Acta 1860: 1309‐1317. These small proteins form ion channels that are of interest because live attenuated vaccines target these channels promising prevention and treatment for coronavirus infections. The SARS coronavirus E channel protein, a right‐handed alpha‐helical bundle, is composed of 5 chains, A through E. Each chain has 16 NMR structures in the database. Incorporating computational and molecular visualization tools students generate data to observe, measure, and communicate the dihedral angle backbone movement of the whole pentamer, the separate chains, and individual amino acid residues on a bond‐by‐bond basis. All the open access software and programs used worked within a Windows/Mac environment except one program that used Linux command lines to create models from the PDB file. Afterwards these models were animated to demonstrate and analyze dihedral angle movement within structures. The students used this work to fulfill the laboratory component of their undergraduate independent study program at in the Biological Sciences and Chemistry Departments of Lehman College, a 4‐year college within the CUNY system.

Irrupciones feministas en el arte antifranquista. La dimensión de lo político en María Franciska Dapena

María Franciska Dapena (1924-1995) fue una artista multidisciplinar vizcaína recordada, por lo general, por su participación –la única femenina– en el colectivo de Estampa Popular de Vizcaya (1962), movimiento vertebrador de la historia del arte del siglo XX español y vasco. No obstante, su reconocimiento como integrante de este proyecto colectivo ha sido fruto de las investigaciones realizadas en las últimasdécadas, donde se ha incorporado el objetivo de recuperar la agencia de mujeres artistas del pasado. En esta ocasión, el artículo trata de analizar, en primer lugar, la figura y obra de Dapena a través de una lectura de género y, a su vez, relacionar parte de su producción con el movimiento feminista que iba tomando forma en los círculos cercanos a la artista donde participaron, por ejemplo, Lidia Falcón o Sol Panera.

Atomistic basis of opening and conduction in mammalian inward rectifier potassium (Kir2.2) channels.

Potassium ion conduction through open potassium channels is essential to control of membrane potentials in all cells. To elucidate the open conformation and hence the mechanism of K+ ion conduction in the classic inward rectifier Kir2.2, we introduced a negative charge (G178D) at the crossing point of the inner helix bundle, the location of ligand-dependent gating. This "forced open" mutation generated channels that were active even in the complete absence of phosphatidylinositol-4,5-bisphosphate (PIP2), an otherwise essential ligand for Kir channel opening. Crystal structures were obtained at a resolution of 3.6 Å without PIP2 bound, or 2.8 Å in complex with PIP2. The latter revealed a slight widening at the helix bundle crossing (HBC) through backbone movement. MD simulations showed that subsequent spontaneous wetting of the pore through the HBC gate region allowed K+ ion movement across the HBC and conduction through the channel. Further simulations reveal atomistic details of the opening process and highlight the role of pore-lining acidic residues in K+ conduction through Kir2 channels.

Structural and molecular basis of angiotensin-converting enzyme by computational modeling: Insights into the mechanisms of different inhibitors.

Angiotensin-I converting enzyme (ACE) is a two-domain dipeptidylcarboxypeptidase involved in regulating blood pressure via the kallikrein-kininand renin-angiotensin-aldosterone complex. Therefore, ACE is a key drug target for the treatment of cardiovascular system diseases. At present many works are focus on searching for new inhibitory peptides of ACE to control the blood pressure. In order to exploit the interactions between ACE and its inhibitors, molecular dynamics simulations were used. The results showed that (a) the secondary structures of the three inhibitor-protein complexes did not change significantly; (b) root-mean-square deviation (RMSD), radius of gyration (Rg), and solvent-accessible surface area (SASA) values of Leu-Ile-Val-Thr (LIVT)-ACE complexes were significantly higher than that of other systems; (c) the backbone movement of LIVT was vigorous in Asp300-Val350, compared with that in Tyr-Leu-Val-Pro-His (YLVPH) and Tyr-Leu-Val-Arg(YLVR), as shown by the center-of-mass distance; and (d) the backbone movement of Asp300-Val350 may contribute to the interaction between ACE and its inhibitors. Our theoretical results will be helpful to further the design of specific inhibitors of ACE.

Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method.

The Farnesoid X receptor (FXR) exhibits significant backbone movement in response to the binding of various ligands and can be a challenge for pose prediction algorithms. As part of the D3R Grand Challenge 2, we tested Wilma-SIE, a rigid-protein docking method, on a set of 36 FXR ligands for which the crystal structures had originally been blinded. These ligands covered several classes of compounds. To overcome the rigid protein limitations of the method, we used an ensemble of publicly available structures for FXR from the PDB. The use of the ensemble allowed Wilma-SIE to predict poses with average and median RMSDs of 2.3 and 1.4Å, respectively. It was quite clear, however, that had we used a single structure for the receptor the success rate would have been much lower. The most successful predictions were obtained on chemical classes for which one or more crystal structures of the receptor bound to a molecule of the same class was available. In the absence of a crystal structure for the class, observing a consensus binding mode for the ligands of the class using one or more receptor structures of other classes seemed to be indicative of a reasonable pose prediction. Affinity prediction proved to be more challenging with generally poor correlation with experimental IC50s (Kendall tau ~ 0.3). Even when the 36 crystal structures were used the accuracy of the predicted affinities was not appreciably improved. A possible cause of difficulty is the internal energy strain arising from conformational differences in the receptor across complexes, which may need to be properly estimated and incorporated into the SIE scoring function.

ROBOT SALAMANDRA ANFIBIO CON LOCOMOCIÓN BIOINSPIRADA

<p>En este artículo se presenta el desarrollo de un robot anfibio con una dinámica de movimiento bioinspirada en la locomoción de la salamandra (Cryptobranchidae). El robot es teleoperado mediante una aplicación para dispositivos móviles (Smartphones, tablets, etc.). Se propone una estructura que permita al robot llevar a cabo dos acciones: caminar y nadar. Los movimientos de una salamandra real se han estimado basándose en una cámara cenital y se ha diseñado un algoritmo de control de locomoción que replique esos movimientos. El desempeño del robot se ha evaluado utilizando como métrica el error cuadrático medio entre el movimiento del robot y de la salamandra obteniendo errores menores al 5 % en los ángulos de movimiento de la espina dorsal.</p>

The flexibility and dynamics of protein disulfide isomerase.

ABSTRACTWe have studied the mobility of the multidomain folding catalyst, protein disulfide isomerase (PDI), by a coarse‐graining approach based on flexibility. We analyze our simulations of yeast PDI (yPDI) using measures of backbone movement, relative positions and orientations of domains, and distances between functional sites. We find that there is interdomain flexibility at every interdomain junction but these show very different characteristics. The extent of interdomain flexibility is such that yPDI's two active sites can approach much more closely than is found in crystal structures—and indeed hinge motion to bring these sites into proximity is the lowest energy normal mode of motion of the protein. The flexibility predicted for yPDI (based on one structure) includes the other known conformation of yPDI and is consistent with (i) the mobility observed experimentally for mammalian PDI and (ii) molecular dynamics. We also observe intradomain flexibility and clear differences between the domains in their propensity for internal motion. Our results suggest that PDI flexibility enables it to interact with many different partner molecules of widely different sizes and shapes, and highlights considerable similarities of yPDI and mammalian PDI. Proteins 2016; 84:1776–1785. © 2016 Wiley Periodicals, Inc.

Quantitative Mapping of Interactions in the Voltage-Sensor Pore Interface of the Shaker Potassium Channel

Changes in the membrane potential of an excitable cell induce movement of voltage-sensing units within voltage-gated ion channels (VGICs). The energy associated with this movement is transmitted to the channel gate, ultimately promoting its opening. Numerous proposals have been made as to how this signal is relayed from the voltage-sensors to the channel gate, such as side chain interactions and backbone movement; however, it has been difficult to ascertain the precise molecular mechanisms underlying energy transduction. Recently, it was shown that median voltage estimates from the charge-voltage relationship of VGICs can be used to derive the net free energy change (ΔGnet) associated with their voltage-dependent activation. By combining this approach with mutant cycle analysis, it is possible to identify residues that are energetically coupled and contribute to the activation process. Here, we have undertaken a systematic analysis of contact pairs at the interface between the voltage-sensor and pore domains of Shaker potassium channel in order to gain insight into how an initial signal can propagate from one region of the channel to another and trigger the opening of the channel gate. Our results will be discussed in the context of overall molecular mechanism of electromechanical coupling in voltage-gated ion channels.

Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.

Advances reported over the last few years and the increasing availability of protein crystal structure data have greatly improved structure-based druggability approaches. However, in practice, nearly all druggability estimation methods are applied to protein crystal structures as rigid proteins, with protein flexibility often not directly addressed. The inclusion of protein flexibility is important in correctly identifying the druggability of pockets that would be missed by methods based solely on the rigid crystal structure. These include cryptic pockets and flexible pockets often found at protein-protein interaction interfaces. Here, we apply an approach that uses protein modeling in concert with druggability estimation to account for light protein backbone movement and protein side-chain flexibility in protein binding sites. We assess the advantages and limitations of this approach on widely-used protein druggability sets. Applying the approach to all mammalian protein crystal structures in the PDB results in identification of 69 proteins with potential druggable cryptic pockets.

The role of the N-terminal loop in the function of the colicin E7 nuclease domain

Colicin E7 (ColE7) is a metallonuclease toxin of Escherichia coli belonging to the HNH superfamily of nucleases. It contains highly conserved amino acids in its HHX(14)NX(8)HX(3)H ββα-type metal ion binding C-terminal active centre. However, the proximity of the arginine at the N-terminus of the nuclease domain of ColE7 (NColE7, 446-576) is necessary for the hydrolytic activity. This poses a possibility of allosteric activation control in this protein. To obtain more information on this phenomenon, two protein mutants were expressed, i.e. four and 25 N-terminal amino acids were removed from NColE7. The effect of the N-terminal truncation on the Zn(2+) ion and DNA binding as well as on the activity was investigated in this study by mass spectrometry, synchrotron-radiation circular dichroism and fluorescence spectroscopy and agarose gel mobility shift assays. The dynamics of protein backbone movement was simulated by molecular dynamics. Semiempirical quantum chemical calculations were performed to obtain better insight into the structure of the active centre. The longer protein interacted with both Zn(2+) ion and DNA more strongly than its shorter counterpart. The results were explained by the structural stabilization effect of the N-terminal amino acids on the catalytic centre. In agreement with this, the absence of the N-terminal sequences resulted in significantly increased movement of the backbone atoms compared with that in the native NColE7: in ΔN25-NColE7 the amino acid strings between residues 485-487, 511-515 and 570-571, and in ΔN4-NColE7 those between residues 467-468, 530-535 and 570-571.

Improved Modeling of Side-Chain–Base Interactions and Plasticity in Protein–DNA Interface Design

Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed “motifs”) was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein–DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent.

Factors That Affect the Computational Prediction of Hot Spots in Protein-Protein Complexes

Protein-protein complexes play an important role in the physiology and the pathology of cellular functions, and therefore are attractive therapeutic targets. A small subset of residues known as “hot spots”, accounts for most of the protein-protein binding free energy. Computational methods play a critical role in identifying the hotspots on the proteinprotein interface. In this paper, we use a computational alanine scanning method with all-atom force fields for predicting hotspots for 313 mutations in 16 protein complexes of known structures. We studied the effect of force fields, solvation models, and conformational sampling on the hotspot predictions. We compared the calculated change in the protein-protein interaction energies upon mutation of the residues in and near the protein-protein interface, to the experimental change in free energies. The AMBER force field (FF) predicted 86% of the hotspots among the three commonly used FF for proteins, namely, AMBER FF, Charmm27 FF, and OPLS-2005 FF. However, AMBER FF also showed a high rate of false positives, while the Charmm27 FF yielded 74% correct predictions of the hotspot residues with low false positives. Van der Waals and hydrogen bonding energy show the largest energy contribution with a high rate of prediction accuracy, while the desolvation energy was found to contribute little to improve the hot spot prediction. Using a conformational ensemble including limited backbone movement instead of one static structure leads to better predicttion of hotpsots.

Does the oestrogen receptor encourage oestrogenicity in environmental pollutants? The case of 4-nonylphenol

A computer-aided docking study was conducted to explore in detail the binding interactions between the structurally unlikely environmental oestrogen 4-nonylphenol (4NP) and three of its metabolites with the human oestrogen receptor alpha (hERα). Docking was done within the Schrodinger Suite 2008 using both a conventional rigid receptor with flexible ligand and the induced-fit docking protocol. Induced-fit docking allows side-chain and backbone movement in the receptor to accommodate the ligand. This study has revealed unconventional interactions between the ligands and the hERα binding pocket that could explain the observed oestrogen-like behaviour of 4NP and suggests some of the metabolites of 4NP may also be oestrogenic.

MOLECULAR DYNAMICS SIMULATION OF POINT MUTATIONS OF ARG 221 IN THE ACTIVE SITE OF PROTEIN TYROSINE PHOSPHATASE 1B

Protein tyrosine phosphatase 1B (PTP1B) is one of the important regulators of signal transduction pathways. The present study aims to investigate the effect of Arg 221 on the active site of PTP1B. Six mutants were carried out using Schrödinger Suite 2007 and molecular dynamics simulation was performed by using the Tinker package. Results show that point mutations at position 221 have great influence on shape of active site, backbone movement of active site, and interaction between substrate and PTP1B. R221H and R221K lead to increased total interaction energies. R221G, R221F and R221T cause increase in total interaction energies, but decrease in interaction energies between pTyr 4 and P loop (catalytic residues). R221E results in both decreased total interaction energies and interaction energies between pTyr 4 and P loop. This indicates that Arg 221 mutated to basic residues can lead to enhanced binding affinity between substrate and protein; when mutated to acidic residues it will decrease binding affinity and catalytic activity; other kinds of mutations result in increased binding affinity but decreased catalytic activity.

Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein

The periplasmic lysine-, arginine-, ornithine-binding protein (LAOBP) traps its ligands by a large hinge bending movement between two globular domains. The overall geometry of the binding site remains largely unchanged between the open (unliganded) and closed (liganded) forms, with only a small number of residues exhibiting limited movement of their side chains. However, in the case of the ornithine-bound structure, the backbone peptide bond between Asp11 and Thr12 undergoes a large rotation. Molecular dynamics simulations have been used to investigate the origin and mechanism of this backbone movement. Simulations allowing flexibility of a limited region and of the whole binding site, with and without bound ligands, suggest that this conformational change is induced by the binding of ornithine, leading to the stabilisation of an energetically favourable alternative conformation.

Large movement in the C terminus of CLC-0 chloride channel during slow gating

Chloride channels and transporters of the CLC gene family are expressed in virtually all cell types and are crucial in the regulation of membrane potential, chloride homeostasis and intravesicular pH. There are two gating processes that open CLC channels-fast and slow. The fast gating process in CLC channels has recently been linked to a small movement of a glutamate side chain. However, the molecular mechanism underlying the slow gating process is still elusive. Using spectroscopic microscopy, we observed a large backbone movement in the C terminus of the CLC-0 chloride channel that was functionally linked to slow gating. We further showed that the C-terminal movement had a time course similar to slow gating. In addition, a mutation known to lock the slow gate open prevented movement of the C terminus. When combined with recent structural information on the CLC C terminus, our findings provide a structural model for understanding the conformational changes linked to slow gating in CLC transport proteins.

Dynamics of hydrogen bonds: how to probe their role in the unusual properties of liquidwater

The dynamics of hydrogen bonds between water molecules is probed by means of coherentquasielastic neutron scattering. The choice of appropriate values of the momentum transfergives information about the time dependence of the DD partial of the scattering function ofD2O. Experimental results demonstrate that the temperature dependence of the dynamics ofhydrogen bonds is weak, in contrast with that of the transport properties of liquid water.We discuss our results in view of a recent application of mode coupling theory to describethe dynamics in polymer melts (Richter et al 1998 Physica B 241–243 1005). In particular,we give arguments in favour of a normal (Arrhenius) temperature dependence ofhydrogen bond dynamics at extremely low temperatures. We relate this dynamics toβ relaxation. This is in contrast to what happens with polymer gels, where theα processes, related to backbone movement, block the molecular motions. The anomalous(non-Arrhenius) temperature dependence of the transport properties of water is thereforedue to the increased number of hydrogen bonds, rather then to their intrinsic dynamics,which remains fast.