Journal articles: 'Molecular dynamics, metalloproteins, structural biology, proteins structure'

1

Cherrier, Mickaël V., Xavier Vernède, Daphna Fenel, Lydie Martin, Benoit Arragain, Emmanuelle Neumann, Juan C. Fontecilla-Camps, Guy Schoehn, and Yvain Nicolet. "Oxygen-Sensitive Metalloprotein Structure Determination by Cryo-Electron Microscopy." Biomolecules 12, no. 3 (March 12, 2022): 441. http://dx.doi.org/10.3390/biom12030441.

Full text

Abstract:

Metalloproteins are involved in key cell processes such as photosynthesis, respiration, and oxygen transport. However, the presence of transition metals (notably iron as a component of [Fe-S] clusters) often makes these proteins sensitive to oxygen-induced degradation. Consequently, their study usually requires strict anaerobic conditions. Although X-ray crystallography has been the method of choice for solving macromolecular structures for many years, recently electron microscopy has also become an increasingly powerful structure-solving technique. We have used our previous experience with cryo-crystallography to develop a method to prepare cryo-EM grids in an anaerobic chamber and have applied it to solve the structures of apoferritin and the 3 [Fe4S4]-containing pyruvate ferredoxin oxidoreductase (PFOR) at 2.40 Å and 2.90 Å resolution, respectively. The maps are of similar quality to the ones obtained under air, thereby validating our method as an improvement in the structural investigation of oxygen-sensitive metalloproteins by cryo-EM.

APA, Harvard, Vancouver, ISO, and other styles

2

Andreini, Claudia, and Antonio Rosato. "Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications." International Journal of Molecular Sciences 23, no. 14 (July 12, 2022): 7684. http://dx.doi.org/10.3390/ijms23147684.

Full text

Abstract:

All living organisms require metal ions for their energy production and metabolic and biosynthetic processes. Within cells, the metal ions involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids). The proteins that require binding to one or more metal ions in order to be able to carry out their physiological function are called metalloproteins. About one third of all protein structures in the Protein Data Bank involve metalloproteins. Over the past few years there has been tremendous progress in the number of computational tools and techniques making use of 3D structural information to support the investigation of metalloproteins. This trend has been boosted by the successful applications of neural networks and machine/deep learning approaches in molecular and structural biology at large. In this review, we discuss recent advances in the development and availability of resources dealing with metalloproteins from a structure-based perspective. We start by addressing tools for the prediction of metal-binding sites (MBSs) using structural information on apo-proteins. Then, we provide an overview of the methods for and lessons learned from the structural comparison of MBSs in a fold-independent manner. We then move to describing databases of metalloprotein/MBS structures. Finally, we summarizing recent ML/DL applications enhancing the functional interpretation of metalloprotein structures.

APA, Harvard, Vancouver, ISO, and other styles

3

Dutagaci, Bercem, Lim Heo, and Michael Feig. "Structure refinement of membrane proteins via molecular dynamics simulations." Proteins: Structure, Function, and Bioinformatics 86, no. 7 (May 6, 2018): 738–50. http://dx.doi.org/10.1002/prot.25508.

Full text

APA, Harvard, Vancouver, ISO, and other styles

4

Öz, Gülin, Dean L. Pountney, and Ian M. Armitage. "NMR spectroscopic studies of I = 1/2 metal ions in biological systems." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 223–34. http://dx.doi.org/10.1139/o98-059.

Full text

Abstract:

This article reviews the use of nuclear magnetic resonance methods of spin 1/2 metal nuclei to probe the metal binding site(s) in a variety of metalloproteins. The majority of the studies have involved native Zn(II) and Ca(II) metalloproteins where there has been isostructural substitution of these metal ions with the I = 1/2 111/113Cd(II) ion. Also included are recent studies that have utilized the 109Ag(I) ion to probe Cu(I) sites in yeast metallothionein and 199Hg(II) as a probe of the metal binding sites in mercury resistance proteins. Pertinent aspects for the optimal execution of these experiments along with the procedures for the metal substitution reactions are discussed together with the presentation of a 113Cd chemical shift correlation map with ligand type and coordination number. Specific examples of protein systems studied using the 111/113Cd and 109Ag nuclei include the metallothionein superfamily of Zn(II)- and Cu(I)-binding proteins from mammalian, invertebrate, and yeast systems. In addition to the structural features revealed by these metal ion nuclear magnetic resonance studies, important new information is frequently provided about the dynamics at the active-site metal ion. In an effort for completeness, other less frequently used spin 1/2 metal nuclei are mentioned.Key words: metallothionein, 111/113Cd, 199Hg, 109Ag, 57Fe, 205Tl, 195Pt, 207Pb, 119Sn, nuclear magnetic resonance.

APA, Harvard, Vancouver, ISO, and other styles

5

Stollar, Elliott J., and David P. Smith. "Uncovering protein structure." Essays in Biochemistry 64, no. 4 (September 25, 2020): 649–80. http://dx.doi.org/10.1042/ebc20190042.

Full text

Abstract:

Abstract Structural biology is the study of the molecular arrangement and dynamics of biological macromolecules, particularly proteins. The resulting structures are then used to help explain how proteins function. This article gives the reader an insight into protein structure and the underlying chemistry and physics that is used to uncover protein structure. We start with the chemistry of amino acids and how they interact within, and between proteins, we also explore the four levels of protein structure and how proteins fold into discrete domains. We consider the thermodynamics of protein folding and why proteins misfold. We look at protein dynamics and how proteins can take on a range of conformations and states. In the second part of this review, we describe the variety of methods biochemists use to uncover the structure and properties of proteins that were described in the first part. Protein structural biology is a relatively new and exciting field that promises to provide atomic-level detail to more and more of the molecules that are fundamental to life processes.

APA, Harvard, Vancouver, ISO, and other styles

6

Rojewska, Danuta, and Ron Elber. "Molecular dynamics study of secondary structure motion in proteins: Application to myohemerythrin." Proteins: Structure, Function, and Genetics 7, no. 3 (1990): 265–79. http://dx.doi.org/10.1002/prot.340070308.

Full text

APA, Harvard, Vancouver, ISO, and other styles

7

Hong, Mei. "Oligomeric Structure, Dynamics, and Orientation of Membrane Proteins from Solid-State NMR." Structure 14, no. 12 (December 2006): 1731–40. http://dx.doi.org/10.1016/j.str.2006.10.002.

Full text

APA, Harvard, Vancouver, ISO, and other styles

8

Gotsmy, Mathias, Yerko Escalona, Chris Oostenbrink, and Drazen Petrov. "Exploring the structure and dynamics of proteins in soil organic matter." Proteins: Structure, Function, and Bioinformatics 89, no. 8 (March 25, 2021): 925–36. http://dx.doi.org/10.1002/prot.26070.

Full text

APA, Harvard, Vancouver, ISO, and other styles

9

Mandala, Venkata S., Jonathan K. Williams, and Mei Hong. "Structure and Dynamics of Membrane Proteins from Solid-State NMR." Annual Review of Biophysics 47, no. 1 (May 20, 2018): 201–22. http://dx.doi.org/10.1146/annurev-biophys-070816-033712.

Full text

Abstract:

Solid-state nuclear magnetic resonance (SSNMR) spectroscopy elucidates membrane protein structures and dynamics in atomic detail to yield mechanistic insights. By interrogating membrane proteins in phospholipid bilayers that closely resemble biological membranes, SSNMR spectroscopists have revealed ion conduction mechanisms, substrate transport dynamics, and oligomeric interfaces of seven-transmembrane helix proteins. Research has also identified conformational plasticity underlying virus-cell membrane fusions by complex protein machineries, and β-sheet folding and assembly by amyloidogenic proteins bound to lipid membranes. These studies collectively show that membrane proteins exhibit extensive structural plasticity to carry out their functions. Because of the inherent dependence of NMR frequencies on molecular orientations and the sensitivity of NMR frequencies to dynamical processes on timescales from nanoseconds to seconds, SSNMR spectroscopy is ideally suited to elucidate such structural plasticity, local and global conformational dynamics, protein-lipid and protein-ligand interactions, and protonation states of polar residues. New sensitivity-enhancement techniques, resolution enhancement by ultrahigh magnetic fields, and the advent of 3D and 4D correlation NMR techniques are increasingly aiding these mechanistically important structural studies.

APA, Harvard, Vancouver, ISO, and other styles

10

Taneishi, Kei, and Yuko Tsuchiya. "Structure-based analyses of gut microbiome-related proteins by neural networks and molecular dynamics simulations." Current Opinion in Structural Biology 73 (April 2022): 102336. http://dx.doi.org/10.1016/j.sbi.2022.102336.

Full text

APA, Harvard, Vancouver, ISO, and other styles

11

Naureen, Irum, Aisha Saleem, Hafiza Hira Rehman, Umar farooq, Iqra Iqbal, Tayyaba Sehar, and Tahir Ali. "Intrinsically Disordered Proteins, Structural and Functional Dynamics." Scholars International Journal of Biochemistry 5, no. 1 (January 21, 2022): 8–14. http://dx.doi.org/10.36348/sijb.2022.v05i01.002.

Full text

Abstract:

The classical theory is that before being biologically active, proteins are assembled into a unique three-dimensional structure in terms of quality. These Intrinsically Disordered Proteins (IDPs) are very common in many genomes, including humans and play a key role in central cell processes such as transcription and translation, cell cycle, and cell signaling regulation. In addition, the proportion of proteins associated with various diseases such as cancer and neurodegenerative diseases is very high in IDPs. Therefore, considerable efforts have been made to elucidate the molecular mechanisms supporting the role of IDPs in Biology and disease through the use of experimental and computational methods. Animal models are needed for human genetic anatomy and better treatment options. Genetic disease Although some animals are used key models in academic and industrial research .There is a lot of stress in the anatomy of genetic diseases. The Genetic resemblance of rats and the humans from which is naturally occurring genetic disease, unique population. The availability of structure and complete genomic sequencing has made purebred dogs a powerful model. Used for disease research. The main advantage of dogs is that they suffer from about 450 genetic diseases, of which about half show significant medical symptoms, Similar to the same human disease. Therefore, these two facts make dogs an ideal medical practice, and a genetic model. This review sheds light on some of them, common genetic disease, in dog model. In this article plays an important role in identifying the genes responsible for the disease and / or the use of new genes, treatment of interest for dogs and humans.

APA, Harvard, Vancouver, ISO, and other styles

12

Hardin, Corey, Zaida Luthey-Schulten, and Peter G. Wolynes. "Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides." Proteins: Structure, Function, and Genetics 34, no. 3 (February 15, 1999): 281–94. http://dx.doi.org/10.1002/(sici)1097-0134(19990215)34:3<281::aid-prot2>3.0.co;2-2.

Full text

APA, Harvard, Vancouver, ISO, and other styles

13

Zamir, Eli, and Benjamin Geiger. "Molecular complexity and dynamics of cell-matrix adhesions." Journal of Cell Science 114, no. 20 (October 15, 2001): 3583–90. http://dx.doi.org/10.1242/jcs.114.20.3583.

Full text

Abstract:

Currently >50 proteins have been reported to be associated with focal contacts and related ECM adhesions. Most of these contain multiple domains through which they can interact with different molecular partners, potentially forming a dense and heterogeneous protein network at the cytoplasmic faces of the adhesion site. The molecular and structural diversity of this ‘submembrane plaque’ is regulated by a wide variety of mechanisms, including competition between different partner proteins for the same binding sites, interactions triggered or suppressed by tyrosine phosphorylation, and conformational changes in component proteins, which can affect their reactivity. Indeed, integrin-mediated adhesions can undergo dynamic changes in structure and molecular properties from dot-like focal complexes to stress-fiber-associated focal contacts, which can further ‘mature’ to form fibronectin-bound fibrillar adhesions. These changes are driven by mechanical force generated by the actin- and myosin-containing contractile machinery of the cells, or by external forces applied to the cells, and regulated by matrix rigidity.

APA, Harvard, Vancouver, ISO, and other styles

14

Gagné, Stéphane M., Monica X. Li, Ryan T. McKay, and Brian D. Sykes. "The NMR angle on troponin C." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 302–12. http://dx.doi.org/10.1139/o98-055.

Full text

Abstract:

The calcium-induced structural changes in the skeletal muscle regulatory protein troponin C involve a transition from a closed to an open structure with the concomitant exposure of a large hydrophobic interaction site for target proteins. NMR solution structural studies have served to define this conformational change and elucidate the mechanism of the linkage between calcium binding and the induced structural changes. These structural movements are described in terms of interhelical angles in these largely helical proteins. Oddly, the most recent structure of the cardiac system challenges the central paradigm because the calcium-bound structures are not open. The kinetics, energetics, and dynamics of these proteins have also been investigated using NMR.Key words: troponin C, calcium binding protein, NMR, structure, energetics.

APA, Harvard, Vancouver, ISO, and other styles

15

Mahajan, Swapnil, Alexandre G. de Brevern, Bernard Offmann, and Narayanaswamy Srinivasan. "Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure." Journal of Biomolecular Structure and Dynamics 32, no. 5 (June 3, 2013): 751–58. http://dx.doi.org/10.1080/07391102.2013.789989.

Full text

APA, Harvard, Vancouver, ISO, and other styles

16

Bertini, Ivano, Donald A. Bryant, Stefano Ciurli, Alexander Dikiy, Claudio O. Fernández, Claudio Luchinat, Niyaz Safarov, Alejandro J. Vila, and Jindong Zhao. "Backbone Dynamics of Plastocyanin in Both Oxidation States." Journal of Biological Chemistry 276, no. 50 (August 16, 2001): 47217–26. http://dx.doi.org/10.1074/jbc.m100304200.

Full text

Abstract:

A model-free analysis based on15NR1,15NR2, and15N-1H nuclear Overhauser effects was performed on reduced (diamagnetic) and oxidized (paramagnetic) forms of plastocyanin fromSynechocystissp. PCC6803. The protein backbone is rigid, displaying a small degree of mobility in the sub-nanosecond time scale. The loops surrounding the copper ion, involved in physiological electron transfer, feature a higher extent of flexibility in the longer time scale in both redox states, as measured from D2O exchange of amide protons and from NH-H2O saturation transfer experiments. In contrast to the situation for other electron transfer proteins, no significant difference in the dynamic properties is found between the two redox forms. A solution structure was also determined for the reduced plastocyanin and compared with the solution structure of the oxidized form in order to assess possible structural changes related to the copper ion redox state. Within the attained resolution, the structure of the reduced plastocyanin is indistinguishable from that of the oxidized form, even though small chemical shift differences are observed. The present characterization provides information on both the structural and dynamic behavior of blue copper proteins in solution that is useful to understand further the role(s) of protein dynamics in electron transfer processes.

APA, Harvard, Vancouver, ISO, and other styles

17

Bolla, Jani R., Francesco Fiorentino, and Carol V. Robinson. "Mass spectrometry informs the structure and dynamics of membrane proteins involved in lipid and drug transport." Current Opinion in Structural Biology 70 (October 2021): 53–60. http://dx.doi.org/10.1016/j.sbi.2021.03.014.

Full text

APA, Harvard, Vancouver, ISO, and other styles

18

Czogalla, Aleksander, Aldona Pieciul, Adam Jezierski, and Aleksander F. Sikorski. "Attaching a spin to a protein -- site-directed spin labeling in structural biology." Acta Biochimica Polonica 54, no. 2 (June 14, 2007): 235–44. http://dx.doi.org/10.18388/abp.2007_3243.

Full text

Abstract:

Site-directed spin labeling and electron paramagnetic resonance spectroscopy have recently experienced an outburst of multiple applications in protein science. Numerous interesting strategies have been introduced for determining the structure of proteins and its conformational changes at the level of the backbone fold. Moreover, considerable technical development in the field makes the technique an attractive approach for the study of structure and dynamics of membrane proteins and large biological complexes at physiological conditions. This review focuses on a brief description of site-directed spin labeling-derived techniques in the context of their recent applications.

APA, Harvard, Vancouver, ISO, and other styles

19

Bitto, Eduard, Craig A. Bingman, Dmitry A. Kondrashov, Jason G. McCoy, Ryan M. Bannen, Gary E. Wesenberg, and George N. Phillips. "Structure and dynamics of γ-SNAP: Insight into flexibility of proteins from the SNAP family." Proteins: Structure, Function, and Bioinformatics 70, no. 1 (July 16, 2007): 93–104. http://dx.doi.org/10.1002/prot.21468.

Full text

APA, Harvard, Vancouver, ISO, and other styles

20

Tverdislov, Vsevolod A., and Ekaterina V. Malyshko. "Chiral Dualism as an Instrument of Hierarchical Structure Formation in Molecular Biology." Symmetry 12, no. 4 (April 8, 2020): 587. http://dx.doi.org/10.3390/sym12040587.

Full text

Abstract:

The origin of chiral asymmetry in biology has attracted the attention of the research community throughout the years. In this paper we discuss the role of chirality and chirality sign alternation (L–D–L–D in proteins and D–L–D–L in DNA) in promoting self-organization in biology, starting at the level of single molecules and continuing to the level of supramolecular assemblies. In addition, we also discuss chiral assemblies in solutions of homochiral organic molecules. Sign-alternating chiral hierarchies created by proteins and nucleic acids are suggested to create the structural basis for the existence of selected mechanical degrees of freedom required for conformational dynamics in enzymes and macromolecular machines.

APA, Harvard, Vancouver, ISO, and other styles

21

Stahlberg, Henning, Andreas Engel, and Ansgar Philippsen. "Assessing the structure of membrane proteins: combining different methods gives the full picture." Biochemistry and Cell Biology 80, no. 5 (October 1, 2002): 563–68. http://dx.doi.org/10.1139/o02-160.

Full text

Abstract:

The rotor stoichiometry of F-ATPases has been revealed by the combined approaches of X-ray diffraction (XRD), electron crystallography, and atomic force microscopy (AFM). XRD showed the rotor from the yeast mitochondrial F-ATPase to contain 10 subunits. AFM was used to visualize the tetradecameric chloroplast rotors, and electron crystallography and AFM together revealed the rotors from Ilyobacter tartaricus to be composed of 11 subunits. While biochemical methods had determined an approximate stoichiometric value, precise measurements and new insights into a species-dependent rotor stoichiometry became available by applying the three structural tools together. The structures of AQP1, a water channel, and GlpF, a glycerol channel, were determined by electron crystallography and XRD. The combination of both of these structural tools with molecular dynamics simulations gave a differentiated description of the mechanisms determining the selectivity of water and glycerol channels. This illustrates that the combination of different methods in structural biology reveals more than each method alone.Key words: AQP1, GlpF, F-ATPase, XRD, electron crystallography, AFM.

APA, Harvard, Vancouver, ISO, and other styles

22

Deyaert, Egon, Margaux Leemans, Ranjan Kumar Singh, Rodrigo Gallardo, Jan Steyaert, Arjan Kortholt, Janelle Lauer, and Wim Versées. "Structure and nucleotide-induced conformational dynamics of the Chlorobium tepidum Roco protein." Biochemical Journal 476, no. 1 (January 7, 2019): 51–66. http://dx.doi.org/10.1042/bcj20180803.

Full text

Abstract:

Abstract The LRR (leucine-rich repeat)–Roc (Ras of complex proteins)–COR (C-terminal of Roc) domains are central to the action of nearly all Roco proteins, including the Parkinson's disease-associated protein LRRK2 (leucine-rich repeat kinase 2). We previously demonstrated that the Roco protein from Chlorobium tepidum (CtRoco) undergoes a dimer–monomer cycle during the GTPase reaction, with the protein being mainly dimeric in the nucleotide-free and GDP (guanosine-5′-diphosphate)-bound states and monomeric in the GTP (guanosine-5′-triphosphate)-bound state. Here, we report a crystal structure of CtRoco in the nucleotide-free state showing for the first time the arrangement of the LRR–Roc–COR. This structure reveals a compact dimeric arrangement and shows an unanticipated intimate interaction between the Roc GTPase domains in the dimer interface, involving residues from the P-loop, the switch II loop, the G4 region and a loop which we named the ‘Roc dimerization loop’. Hydrogen–deuterium exchange coupled to mass spectrometry (HDX-MS) is subsequently used to highlight structural alterations induced by individual steps along the GTPase cycle. The structure and HDX-MS data propose a pathway linking nucleotide binding to monomerization and relaying the conformational changes via the Roc switch II to the LRR and COR domains. Together, this work provides important new insights in the regulation of the Roco proteins.

APA, Harvard, Vancouver, ISO, and other styles

23

Hirokawa, Nobutaka, and Yasuko Noda. "Intracellular Transport and Kinesin Superfamily Proteins, KIFs: Structure, Function, and Dynamics." Physiological Reviews 88, no. 3 (July 2008): 1089–118. http://dx.doi.org/10.1152/physrev.00023.2007.

Full text

Abstract:

Various molecular cell biology and molecular genetic approaches have indicated significant roles for kinesin superfamily proteins (KIFs) in intracellular transport and have shown that they are critical for cellular morphogenesis, functioning, and survival. KIFs not only transport various membrane organelles, protein complexes, and mRNAs for the maintenance of basic cellular activity, but also play significant roles for various mechanisms fundamental for life, such as brain wiring, higher brain functions such as memory and learning and activity-dependent neuronal survival during brain development, and for the determination of important developmental processes such as left-right asymmetry formation and suppression of tumorigenesis. Accumulating data have revealed a molecular mechanism of cargo recognition involving scaffolding or adaptor protein complexes. Intramolecular folding and phosphorylation also regulate the binding activity of motor proteins. New techniques using molecular biophysics, cryoelectron microscopy, and X-ray crystallography have detected structural changes in motor proteins, synchronized with ATP hydrolysis cycles, leading to the development of independent models of monomer and dimer motors for processive movement along microtubules.

APA, Harvard, Vancouver, ISO, and other styles

24

Škulj, Sanja, Zlatko Brkljača, Jürgen Kreiter, Elena E. Pohl, and Mario Vazdar. "Molecular Dynamics Simulations of Mitochondrial Uncoupling Protein 2." International Journal of Molecular Sciences 22, no. 3 (January 26, 2021): 1214. http://dx.doi.org/10.3390/ijms22031214.

Full text

Abstract:

Molecular dynamics (MD) simulations of uncoupling proteins (UCP), a class of transmembrane proteins relevant for proton transport across inner mitochondrial membranes, represent a complicated task due to the lack of available structural data. In this work, we use a combination of homology modelling and subsequent microsecond molecular dynamics simulations of UCP2 in the DOPC phospholipid bilayer, starting from the structure of the mitochondrial ATP/ADP carrier (ANT) as a template. We show that this protocol leads to a structure that is impermeable to water, in contrast to MD simulations of UCP2 structures based on the experimental NMR structure. We also show that ATP binding in the UCP2 cavity is tight in the homology modelled structure of UCP2 in agreement with experimental observations. Finally, we corroborate our results with conductance measurements in model membranes, which further suggest that the UCP2 structure modeled from ANT protein possesses additional key functional elements, such as a fatty acid-binding site at the R60 region of the protein, directly related to the proton transport mechanism across inner mitochondrial membranes.

APA, Harvard, Vancouver, ISO, and other styles

25

Ohkubo, Tatsunari, Takaaki Shiina, Kayoko Kawaguchi, Daisuke Sasaki, Rena Inamasu, Yue Yang, Zhuoqi Li, et al. "Visualizing Intramolecular Dynamics of Membrane Proteins." International Journal of Molecular Sciences 23, no. 23 (November 22, 2022): 14539. http://dx.doi.org/10.3390/ijms232314539.

Full text

Abstract:

Membrane proteins play important roles in biological functions, with accompanying allosteric structure changes. Understanding intramolecular dynamics helps elucidate catalytic mechanisms and develop new drugs. In contrast to the various technologies for structural analysis, methods for analyzing intramolecular dynamics are limited. Single-molecule measurements using optical microscopy have been widely used for kinetic analysis. Recently, improvements in detectors and image analysis technology have made it possible to use single-molecule determination methods using X-rays and electron beams, such as diffracted X-ray tracking (DXT), X-ray free electron laser (XFEL) imaging, and cryo-electron microscopy (cryo-EM). High-speed atomic force microscopy (HS-AFM) is a scanning probe microscope that can capture the structural dynamics of biomolecules in real time at the single-molecule level. Time-resolved techniques also facilitate an understanding of real-time intramolecular processes during chemical reactions. In this review, recent advances in membrane protein dynamics visualization techniques were presented.

APA, Harvard, Vancouver, ISO, and other styles

26

Panigrahi, Rashmi, and J. N. Mark Glover. "Structural insights into DNA double-strand break signaling." Biochemical Journal 478, no. 1 (January 13, 2021): 135–56. http://dx.doi.org/10.1042/bcj20200066.

Full text

Abstract:

Genomic integrity is most threatened by double-strand breaks, which, if left unrepaired, lead to carcinogenesis or cell death. The cell generates a network of protein–protein signaling interactions that emanate from the DNA damage which are now recognized as a rich basis for anti-cancer therapy development. Deciphering the structures of signaling proteins has been an uphill task owing to their large size and complex domain organization. Recent advances in mammalian protein expression/purification and cryo-EM-based structure determination have led to significant progress in our understanding of these large multidomain proteins. This review is an overview of the structural principles that underlie some of the key signaling proteins that function at the double-strand break site. We also discuss some plausible ideas that could be considered for future structural approaches to visualize and build a more complete understanding of protein dynamics at the break site.

APA, Harvard, Vancouver, ISO, and other styles

27

Tzotzos, George. "A Comparative Evaluation of the Structural and Dynamic Properties of Insect Odorant Binding Proteins." Biomolecules 12, no. 2 (February 9, 2022): 282. http://dx.doi.org/10.3390/biom12020282.

Full text

Abstract:

Insects devote a major part of their metabolic resources to the production of odorant binding proteins (OBPs). Although initially, these proteins were implicated in the solubilisation, binding and transport of semiochemicals to olfactory receptors, it is now recognised that they may play diverse, as yet uncharacterised, roles in insect physiology. The structures of these OBPs, the majority of which are known as “classical” OBPs, have shed some light on their potential functional roles. However, the dynamic properties of these proteins have received little attention despite their functional importance. Structural dynamics are encoded in the native protein fold and enable the adaptation of proteins to substrate binding. This paper provides a comparative review of the structural and dynamic properties of OBPs, making use of sequence/structure analysis, statistical and theoretical physics-based methods. It provides a new layer of information and additional methodological tools useful in unravelling the relationship between structure, dynamics and function of insect OBPs. The dynamic properties of OBPs, studied by means of elastic network models, reflect the similarities/dissimilarities observed in their respective structures and provides insights regarding protein motions that may have important implications for ligand recognition and binding. Furthermore, it was shown that the OBPs studied in this paper share conserved structural ‘core’ that may be of evolutionary and functional importance.

APA, Harvard, Vancouver, ISO, and other styles

28

Kaluarachchi, Kumaralal, David G. Gorenstein, and Bruce A. Luxon. "How Do Proteins Recognize DNA? Solution Structure and Local Conformational Dynamics ofLacOperators by 2D NMR." Journal of Biomolecular Structure and Dynamics 17, sup1 (January 2000): 123–33. http://dx.doi.org/10.1080/07391102.2000.10506612.

Full text

APA, Harvard, Vancouver, ISO, and other styles

29

Magyar, Csaba, Bálint Zoltán Németh, Miklós Cserző, and István Simon. "Molecular Dynamics Simulation as a Tool to Identify Mutual Synergistic Folding Proteins." International Journal of Molecular Sciences 24, no. 2 (January 16, 2023): 1790. http://dx.doi.org/10.3390/ijms24021790.

Full text

Abstract:

Mutual synergistic folding (MSF) proteins belong to a recently emerged subclass of disordered proteins, which are disordered in their monomeric forms but become ordered in their oligomeric forms. They can be identified by experimental methods following their unfolding, which happens in a single-step cooperative process, without the presence of stable monomeric intermediates. Only a limited number of experimentally validated MSF proteins are accessible. The amino acid composition of MSF proteins shows high similarity to globular ordered proteins, rather than to disordered ones. However, they have some special structural features, which makes it possible to distinguish them from globular proteins. Even in the possession of their oligomeric three-dimensional structure, classification can only be performed based on unfolding experiments, which are frequently absent. In this work, we demonstrate a simple protocol using molecular dynamics simulations, which is able to indicate that a protein structure belongs to the MSF subclass. The presumption of the known atomic resolution quaternary structure is an obvious limitation of the method, and because of its high computational time requirements, it is not suitable for screening large databases; still, it is a valuable in silico tool for identification of MSF proteins.

APA, Harvard, Vancouver, ISO, and other styles

30

Mookherjee, Debdatto, Priyanka Majumder, Rukmini Mukherjee, Debmita Chatterjee, Zenia Kaul, Subhrangshu Das, Rachid Sougrat, Saikat Chakrabarti, and Oishee Chakrabarti. "Cytosolic aggregates in presence of non‐translocated proteins perturb endoplasmic reticulum structure and dynamics." Traffic 20, no. 12 (October 2019): 943–60. http://dx.doi.org/10.1111/tra.12694.

Full text

APA, Harvard, Vancouver, ISO, and other styles

31

Kalathiya, Umesh, Monikaben Padariya, Jakub Faktor, Etienne Coyaud, Javier A. Alfaro, Robin Fahraeus, Ted R. Hupp, and David R. Goodlett. "Interfaces with Structure Dynamics of the Workhorses from Cells Revealed through Cross-Linking Mass Spectrometry (CLMS)." Biomolecules 11, no. 3 (March 4, 2021): 382. http://dx.doi.org/10.3390/biom11030382.

Full text

Abstract:

The fundamentals of how protein–protein/RNA/DNA interactions influence the structures and functions of the workhorses from the cells have been well documented in the 20th century. A diverse set of methods exist to determine such interactions between different components, particularly, the mass spectrometry (MS) methods, with its advanced instrumentation, has become a significant approach to analyze a diverse range of biomolecules, as well as bring insights to their biomolecular processes. This review highlights the principal role of chemistry in MS-based structural proteomics approaches, with a particular focus on the chemical cross-linking of protein–protein/DNA/RNA complexes. In addition, we discuss different methods to prepare the cross-linked samples for MS analysis and tools to identify cross-linked peptides. Cross-linking mass spectrometry (CLMS) holds promise to identify interaction sites in larger and more complex biological systems. The typical CLMS workflow allows for the measurement of the proximity in three-dimensional space of amino acids, identifying proteins in direct contact with DNA or RNA, and it provides information on the folds of proteins as well as their topology in the complexes. Principal CLMS applications, its notable successes, as well as common pipelines that bridge proteomics, molecular biology, structural systems biology, and interactomics are outlined.

APA, Harvard, Vancouver, ISO, and other styles

32

Khakzad, Hamed, Lotta Happonen, Yasaman Karami, Sounak Chowdhury, Gizem Ertürk Bergdahl, Michael Nilges, Guy Tran Van Nhieu, Johan Malmström, and Lars Malmström. "Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology." PLOS Computational Biology 17, no. 1 (January 7, 2021): e1008169. http://dx.doi.org/10.1371/journal.pcbi.1008169.

Full text

Abstract:

Streptococcus pyogenes (Group A streptococcus; GAS) is an important human pathogen responsible for mild to severe, life-threatening infections. GAS expresses a wide range of virulence factors, including the M family proteins. The M proteins allow the bacteria to evade parts of the human immune defenses by triggering the formation of a dense coat of plasma proteins surrounding the bacteria, including IgGs. However, the molecular level details of the M1-IgG interaction have remained unclear. Here, we characterized the structure and dynamics of this interaction interface in human plasma on the surface of live bacteria using integrative structural biology, combining cross-linking mass spectrometry and molecular dynamics (MD) simulations. We show that the primary interaction is formed between the S-domain of M1 and the conserved IgG Fc-domain. In addition, we show evidence for a so far uncharacterized interaction between the A-domain and the IgG Fc-domain. Both these interactions mimic the protein G-IgG interface of group C and G streptococcus. These findings underline a conserved scavenging mechanism used by GAS surface proteins that block the IgG-receptor (FcγR) to inhibit phagocytic killing. We additionally show that we can capture Fab-bound IgGs in a complex background and identify XLs between the constant region of the Fab-domain and certain regions of the M1 protein engaged in the Fab-mediated binding. Our results elucidate the M1-IgG interaction network involved in inhibition of phagocytosis and reveal important M1 peptides that can be further investigated as future vaccine targets.

APA, Harvard, Vancouver, ISO, and other styles

33

Saiz, Leonor, Sanjoy Bandyopadhyay, and Michael L. Klein. "Towards an Understanding of Complex Biological Membranes from Atomistic Molecular Dynamics Simulations." Bioscience Reports 22, no. 2 (April 1, 2002): 151–73. http://dx.doi.org/10.1023/a:1020130420869.

Full text

Abstract:

Computer simulation has emerged as a powerful tool for studying the structural and functional properties of complex biological membranes. In the last few years, the use of recently developed simulation methodologies and current generation force fields has permitted novel applications of molecular dynamics simulations, which have enhanced our understanding of the different physical processes governing biomembrane structure and dynamics. This review focuses on frontier areas of research with important biomedical applications. We have paid special attention to polyunsaturated lipids, membrane proteins and ion channels, surfactant additives in membranes, and lipid–DNA gene transfer complexes.

APA, Harvard, Vancouver, ISO, and other styles

34

Arnittali, Maria, Anastassia N. Rissanou, Maria Amprazi, Michael Kokkinidis, and Vagelis Harmandaris. "Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments." International Journal of Molecular Sciences 22, no. 11 (May 31, 2021): 5931. http://dx.doi.org/10.3390/ijms22115931.

Full text

Abstract:

In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states. Then, the thermal stability of both proteins is explored showing RM6 as more thermostable than wtRop through all studied measures. Deviations from native structures are detected mostly in tails and loop regions and most flexible residues are indicated. Decrease of hydrogen bonds with the increase of temperature is observed, as well as reduction of hydrophobic contacts in both proteins. Experimental data from circular dichroism spectroscopy (CD), are also presented, highlighting the effect of temperature on the structural integrity of wtRop and RM6. The central goal of this study is to explore on the atomic level how a protein mutation can cause major changes in its physical properties, like its structural stability.

APA, Harvard, Vancouver, ISO, and other styles

35

Herold, Nadine, Cindy L. Will, Elmar Wolf, Berthold Kastner, Henning Urlaub, and Reinhard Lührmann. "Conservation of the Protein Composition and Electron Microscopy Structure of Drosophila melanogaster and Human Spliceosomal Complexes." Molecular and Cellular Biology 29, no. 1 (November 3, 2008): 281–301. http://dx.doi.org/10.1128/mcb.01415-08.

Full text

Abstract:

ABSTRACT Comprehensive proteomics analyses of spliceosomal complexes are currently limited to those in humans, and thus, it is unclear to what extent the spliceosome's highly complex composition and compositional dynamics are conserved among metazoans. Here we affinity purified Drosophila melanogaster spliceosomal B and C complexes formed in Kc cell nuclear extract. Mass spectrometry revealed that their composition is highly similar to that of human B and C complexes. Nonetheless, a number of Drosophila-specific proteins were identified, suggesting that there may be novel factors contributing specifically to splicing in flies. Protein recruitment and release events during the B-to-C transition were also very similar in both organisms. Electron microscopy of Drosophila B complexes revealed a high degree of structural similarity with human B complexes, indicating that higher-order interactions are also largely conserved. A comparison of Drosophila spliceosomes formed on a short versus long intron revealed only small differences in protein composition but, nonetheless, clear structural differences under the electron microscope. Finally, the characterization of affinity-purified Drosophila mRNPs indicated that exon junction complex proteins are recruited in a splicing-dependent manner during C complex formation. These studies provide insights into the evolutionarily conserved composition and structure of the metazoan spliceosome, as well as its compositional dynamics during catalytic activation.

APA, Harvard, Vancouver, ISO, and other styles

36

Li, Qingxin, and Congbao Kang. "Structure and Dynamics of Zika Virus Protease and Its Insights into Inhibitor Design." Biomedicines 9, no. 8 (August 19, 2021): 1044. http://dx.doi.org/10.3390/biomedicines9081044.

Full text

Abstract:

Zika virus (ZIKV)—a member of the Flaviviridae family—is an important human pathogen. Its genome encodes a polyprotein that can be further processed into structural and non-structural proteins. ZIKV protease is an important target for antiviral development due to its role in cleaving the polyprotein to release functional viral proteins. The viral protease is a two-component protein complex formed by NS2B and NS3. Structural studies using different approaches demonstrate that conformational changes exist in the protease. The structures and dynamics of this protease in the absence and presence of inhibitors were explored to provide insights into the inhibitor design. The dynamic nature of residues binding to the enzyme cleavage site might be important for the function of the protease. Due to the charges at the protease cleavage site, it is challenging to develop small-molecule compounds acting as substrate competitors. Developing small-molecule compounds to inhibit protease activity through an allosteric mechanism is a feasible strategy because conformational changes are observed in the protease. Herein, structures and dynamics of ZIKV protease are summarized. The conformational changes of ZIKV protease and other proteases in the same family are discussed. The progress in developing allosteric inhibitors is also described. Understanding the structures and dynamics of the proteases are important for designing potent inhibitors.

APA, Harvard, Vancouver, ISO, and other styles

37

Fang, Chong, and Longteng Tang. "Mapping Structural Dynamics of Proteins with Femtosecond Stimulated Raman Spectroscopy." Annual Review of Physical Chemistry 71, no. 1 (April 20, 2020): 239–65. http://dx.doi.org/10.1146/annurev-physchem-071119-040154.

Full text

Abstract:

The structure–function relationships of biomolecules have captured the interest and imagination of the scientific community and general public since the field of structural biology emerged to enable the molecular understanding of life processes. Proteins that play numerous functional roles in cellular processes have remained in the forefront of research, inspiring new characterization techniques. In this review, we present key theoretical concepts and recent experimental strategies using femtosecond stimulated Raman spectroscopy (FSRS) to map the structural dynamics of proteins, highlighting the flexible chromophores on ultrafast timescales. In particular, wavelength-tunable FSRS exploits dynamic resonance conditions to track transient-species-dependent vibrational motions, enabling rational design to alter functions. Various ways of capturing excited-state chromophore structural snapshots in the time and/or frequency domains are discussed. Continuous development of experimental methodologies, synergistic correlation with theoretical modeling, and the expansion to other nonequilibrium, photoswitchable, and controllable protein systems will greatly advance the chemical, physical, and biological sciences.

APA, Harvard, Vancouver, ISO, and other styles

38

Tokunaga, Yuji, Thibault Viennet, Haribabu Arthanari, and Koh Takeuchi. "Spotlight on the Ballet of Proteins: The Structural Dynamic Properties of Proteins Illuminated by Solution NMR." International Journal of Molecular Sciences 21, no. 5 (March 6, 2020): 1829. http://dx.doi.org/10.3390/ijms21051829.

Full text

Abstract:

Solution NMR spectroscopy is a unique and powerful technique that has the ability to directly connect the structural dynamics of proteins in physiological conditions to their activity and function. Here, we summarize recent studies in which solution NMR contributed to the discovery of relationships between key dynamic properties of proteins and functional mechanisms in important biological systems. The capacity of NMR to quantify the dynamics of proteins over a range of time scales and to detect lowly populated protein conformations plays a critical role in its power to unveil functional protein dynamics. This analysis of dynamics is not only important for the understanding of biological function, but also in the design of specific ligands for pharmacologically important proteins. Thus, the dynamic view of structure provided by NMR is of importance in both basic and applied biology.

APA, Harvard, Vancouver, ISO, and other styles

39

Knorre, D. G. "Physicochemical Biology: Conquered Boundaries and New Horizons." Acta Naturae 4, no. 2 (June 15, 2012): 36–43. http://dx.doi.org/10.32607/20758251-2012-4-2-36-43.

Full text

Abstract:

In this paper, we shall consider the main evolutionary stages that occurred within the field of physicochemical biology during the 20th century, following the determination of the tertiary structure of DNA by Watson and Crick and the subsequent successes in the X-ray structural analysis of biopolymers. The authors ideas on the pre-emptive problems and the methods used in physicochemical biology in the 21st century are also presented, including an investigation of the dynamics of biochemical processes, studies of the functions of unstructured proteins, as well as single-molecule investigations of enzymatic processes and of biopolymer tertiary structure formation.

APA, Harvard, Vancouver, ISO, and other styles

40

Knorre, D. G. "Physicochemical Biology: Conquered Boundaries and New Horizons." Acta Naturae 4, no. 2 (June 15, 2012): 36–43. http://dx.doi.org/10.32607/actanaturae.10624.

Full text

Abstract:

In this paper, we shall consider the main evolutionary stages that occurred within the field of physicochemical biology during the 20th century, following the determination of the tertiary structure of DNA by Watson and Crick and the subsequent successes in the X-ray structural analysis of biopolymers. The authors ideas on the pre-emptive problems and the methods used in physicochemical biology in the 21st century are also presented, including an investigation of the dynamics of biochemical processes, studies of the functions of unstructured proteins, as well as single-molecule investigations of enzymatic processes and of biopolymer tertiary structure formation.

APA, Harvard, Vancouver, ISO, and other styles

41

Belato, Helen B., and George P. Lisi. "The Many (Inter)faces of Anti-CRISPRs: Modulation of CRISPR-Cas Structure and Dynamics by Mechanistically Diverse Inhibitors." Biomolecules 13, no. 2 (January 31, 2023): 264. http://dx.doi.org/10.3390/biom13020264.

Full text

Abstract:

The discovery of protein inhibitors of CRISPR-Cas systems, called anti-CRISPRs (Acrs), has enabled the development of highly controllable and precise CRISPR-Cas tools. Anti-CRISPRs share very little structural or sequential resemblance to each other or to other proteins, which raises intriguing questions regarding their modes of action. Many structure–function studies have shed light on the mechanism(s) of Acrs, which can act as orthosteric or allosteric inhibitors of CRISPR–Cas machinery, as well as enzymes that irreversibly modify CRISPR–Cas components. Only recently has the breadth of diversity of Acr structures and functions come to light, and this remains a rapidly evolving field. Here, we draw attention to a plethora of Acr mechanisms, with particular focus on how their action toward Cas proteins modulates conformation, dynamic (allosteric) signaling, nucleic acid binding, and cleavage ability.

APA, Harvard, Vancouver, ISO, and other styles

42

Oh, Kwang-Im, Jinwoo Kim, Chin-Ju Park, and Joon-Hwa Lee. "Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy." International Journal of Molecular Sciences 21, no. 8 (April 11, 2020): 2673. http://dx.doi.org/10.3390/ijms21082673.

Full text

Abstract:

The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.

APA, Harvard, Vancouver, ISO, and other styles

43

Duong, Vy T., Elizabeth M. Diessner, Gianmarc Grazioli, Rachel W. Martin, and Carter T. Butts. "Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures." Biomolecules 11, no. 12 (November 30, 2021): 1788. http://dx.doi.org/10.3390/biom11121788.

Full text

Abstract:

Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a particularly useful way of obtaining highly compressed representations of molecular structures, and simulations operating via such representations can achieve substantial computational savings. A drawback of coarse-graining, however, is the loss of atomistic detail—an effect that is especially acute for topological representations such as protein structure networks (PSNs). Here, we introduce an approach based on a combination of machine learning and physically-guided refinement for inferring atomic coordinates from PSNs. This “neural upscaling” procedure exploits the constraints implied by PSNs on possible configurations, as well as differences in the likelihood of observing different configurations with the same PSN. Using a 1 μs atomistic molecular dynamics trajectory of Aβ1–40, we show that neural upscaling is able to effectively recapitulate detailed structural information for intrinsically disordered proteins, being particularly successful in recovering features such as transient secondary structure. These results suggest that scalable network-based models for protein structure and dynamics may be used in settings where atomistic detail is desired, with upscaling employed to impute atomic coordinates from PSNs.

APA, Harvard, Vancouver, ISO, and other styles

44

Kang, Hyun-Seo, and Michael Sattler. "Capturing dynamic conformational shifts in protein–ligand recognition using integrative structural biology in solution." Emerging Topics in Life Sciences 2, no. 1 (April 20, 2018): 107–19. http://dx.doi.org/10.1042/etls20170090.

Full text

Abstract:

In recent years, a dynamic view of the structure and function of biological macromolecules is emerging, highlighting an essential role of dynamic conformational equilibria to understand molecular mechanisms of biological functions. The structure of a biomolecule, i.e. protein or nucleic acid in solution, is often best described as a dynamic ensemble of conformations, rather than a single structural state. Strikingly, the molecular interactions and functions of the biological macromolecule can then involve a shift between conformations that pre-exist in such an ensemble. Upon external cues, such population shifts of pre-existing conformations allow gradually relaying the signal to the downstream biological events. An inherent feature of this principle is conformational dynamics, where intrinsically disordered regions often play important roles to modulate the conformational ensemble. Unequivocally, solution-state NMR spectroscopy is a powerful technique to study the structure and dynamics of such biomolecules in solution. NMR is increasingly combined with complementary techniques, including fluorescence spectroscopy and small angle scattering. The combination of these techniques provides complementary information about the conformation and dynamics in solution and thus affords a comprehensive description of biomolecular functions and regulations. Here, we illustrate how an integrated approach combining complementary techniques can assess the structure and dynamics of proteins and protein complexes in solution.

APA, Harvard, Vancouver, ISO, and other styles

45

Ding, Xiaoyan, Xin Zhao, and Anthony Watts. "G-protein-coupled receptor structure, ligand binding and activation as studied by solid-state NMR spectroscopy." Biochemical Journal 450, no. 3 (February 28, 2013): 443–57. http://dx.doi.org/10.1042/bj20121644.

Full text

Abstract:

GPCRs (G-protein-coupled receptors) are versatile signalling molecules at the cell surface and make up the largest and most diverse family of membrane receptors in the human genome. They convert a large variety of extracellular stimuli into intracellular responses through the activation of heterotrimeric G-proteins, which make them key regulatory elements in a broad range of normal and pathological processes, and are therefore one of the most important targets for pharmaceutical drug discovery. Knowledge of a GPCR structure enables us to gain a mechanistic insight into its function and dynamics, and further aid rational drug design. Despite intensive research carried out over the last three decades, resolving the structural basis of GPCR function is still a major activity. The crystal structures obtained in the last 5 years provide the first opportunity to understand how protein structure dictates the unique functional properties of these complex signalling molecules. However, owing to the intrinsic hydrophobicity, flexibility and instability of membrane proteins, it is still a challenge to crystallize GPCRs, and, when this is possible, it is no longer in its native membrane environment and no longer without modification. Furthermore, the conformational change of the transmembrane α-helices associated with the structure activation increases the difficulty of capturing the activation state of a GPCR to a higher resolution by X-ray crystallography. On the other hand, solid-state NMR may offer a unique opportunity to study membrane protein structure, ligand binding and activation at atomic resolution in the native membrane environment, as well as described functionally significant dynamics. In the present review, we discuss some recent achievements of solid-state NMR for understanding GPCRs, the largest mammalian proteome at ~1% of the total expressed proteins. Structural information, details of determination, details of ligand conformations and the consequences of ligand binding to initiate activation can all be explored with solid-state NMR.

APA, Harvard, Vancouver, ISO, and other styles

46

Hirokawa, N. "From electron microscopy to molecular cell biology, molecular genetics and structural biology: intracellular transport and kinesin superfamily proteins, KIFs: genes, structure, dynamics and functions." Microscopy 60, suppl 1 (August 1, 2011): S63—S92. http://dx.doi.org/10.1093/jmicro/dfr051.

Full text

APA, Harvard, Vancouver, ISO, and other styles

47

Kovaleva, Valentina, Irina Bukhteeva, Oleg Y. Kit, and Irina V. Nesmelova. "Plant Defensins from a Structural Perspective." International Journal of Molecular Sciences 21, no. 15 (July 26, 2020): 5307. http://dx.doi.org/10.3390/ijms21155307.

Full text

Abstract:

Plant defensins form a family of proteins with a broad spectrum of protective activities against fungi, bacteria, and insects. Furthermore, some plant defensins have revealed anticancer activity. In general, plant defensins are non-toxic to plant and mammalian cells, and interest in using them for biotechnological and medicinal purposes is growing. Recent studies provided significant insights into the mechanisms of action of plant defensins. In this review, we focus on structural and dynamics aspects and discuss structure-dynamics-function relations of plant defensins.

APA, Harvard, Vancouver, ISO, and other styles

48

Ray-Gallet, Dominique, and Geneviève Almouzni. "Nucleosome dynamics and histone variants." Essays in Biochemistry 48 (September 20, 2010): 75–87. http://dx.doi.org/10.1042/bse0480075.

Full text

Abstract:

In eukaryotes, DNA is organized into chromatin, a dynamic structure that enables DNA to be accessed for processes such as transcription, replication and repair. To form, maintain or alter this organization according to cellular needs, histones, the main protein component of chromatin, are deposited, replaced, exchanged and post-translationally modified. Histone variants, which exhibit specialized deposition modes in relation to the cell cycle and possibly particular chromatin regions, add an additional level of complexity in the regulation of histone flow. During their metabolism, from their synthesis to their delivery for nucleosome formation, the histones are escorted by proteins called histone chaperones. In the present chapter we summarize our current knowledge concerning histone chaperones and their interaction with particular histones based on key structural properties. From a compilation of selected histone chaperones identified to date, we discuss how they may be placed in a network to regulate histone dynamics. Finally, we provide working models to explain how H3 variants, deposited on to DNA using different histone chaperone machineries, can be transmitted or lost through cell divisions.

APA, Harvard, Vancouver, ISO, and other styles

49

Siminovitch, David J. "Solid-state NMR studies of proteins: the view from static 2H NMR experiments." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 411–22. http://dx.doi.org/10.1139/o98-054.

Full text

Abstract:

The application of solid-state 2H NMR spectroscopy to the study of protein and peptide structure and dynamics is reviewed. The advantages of solid-state NMR for the study of proteins are considered, and the particular advantages of solid-state 2H NMR are summarized. Examples of work on the integral membrane protein bacteriorhodopsin, and the membrane peptide gramicidin, are used to highlight the major achievements of the 2H NMR technique. These examples demonstrate that through the use of oriented samples, it is possible to obtain both structural and dynamic information simultaneously.Key words: solid-state NMR, 2H NMR, membrane peptides, membrane proteins, oriented bilayers.

APA, Harvard, Vancouver, ISO, and other styles

50

Lakomek, Nils-Alexander. "Biologische Festkörper-NMR-Spektroskopie in der Strukturbiologie." BIOspektrum 27, no. 3 (May 2021): 257–59. http://dx.doi.org/10.1007/s12268-021-1561-0.

Full text

Abstract:

AbstractBiological solid-state NMR elucidates the structure and dynamics of biomolecules at physiological temperatures. It provides high-resolution structural information for a wide range of biomolecules and assemblies, from small membrane proteins embedded in a lipid environment, over fibrillar structures up to supramolecular assemblies. Recent developments allow for proton detection at fast magic angle spinning frequencies, which reduces the required sample amounts to a few hundreds of micrograms.

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'Molecular dynamics, metalloproteins, structural biology, proteins structure'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles