Relevant bibliographies by topics / Molecular dynamics, metalloproteins, structural biology, proteins structure

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
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Academic literature on the topic 'Molecular dynamics, metalloproteins, structural biology, proteins structure'

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Published: 10 March 2023

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

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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.

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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.
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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.

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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.
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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.

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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.

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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.
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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.

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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.
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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.

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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.

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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.

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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.

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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.
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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.

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Dissertations / Theses on the topic "Molecular dynamics, metalloproteins, structural biology, proteins structure"

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Sahakyan, Aleksandr B. "Extending the boundaries of the usage of NMR chemical shifts in deciphering biomolecular structure and dynamics." Thesis, University of Cambridge, 2012. https://www.repository.cam.ac.uk/handle/1810/243642.

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NMR chemical shifts have an extremely high information content on the behaviour of macromolecules, owing to their non-trivial dependence on myriads of structural and environmental factors. Although such complex dependence creates an initial barrier for their use for the characterisation of the structures of protein and nucleic acids, recent developments in prediction methodologies and their successful implementation in resolving the structures of these molecules have clearly demonstrated that such barrier can be crossed. Furthermore, the significance of chemical shifts as useful observables in their own right has been substantially increased since the development of the NMR techniques to study low populated 'excited' states of biomolecules. This work is aimed at increasing our understanding of the multiple factors that affect chemical shifts in proteins and nucleic acids, and at developing high-quality chemical shift predictors for atom types that so far have largely escaped the attention in chemical shift restrained molecular dynamics simulations. A general approach is developed to optimise the models for structure-based chemical shift prediction, which is then used to construct CH3Shift and ArShift chemical shift predictors for the nuclei of protein side-chain methyl and aromatic moieties. These results have the potential of making a significant impact in structural biology, in particular when taking into account the advent of recent techniques for specific isotope labelling of protein side-chain atoms, which make large biomolecules accessible to NMR techniques. Through their incorporation as restraints in molecular dynamics simulations, the chemical shifts predicted by the approach described in this work create the opportunity of studying the structure and dynamics of proteins in a wide range of native and non-native states in order to characterise the mechanisms underlying the function and dysfunction of these molecules.
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Ozen, Aysegul. "Structure and Dynamics of Viral Substrate Recognition and Drug Resistance: A Dissertation." eScholarship@UMMS, 2013. https://escholarship.umassmed.edu/gsbs_diss/677.

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Drug resistance is a major problem in quickly evolving diseases, including the human immunodeficiency (HIV) and hepatitis C viral (HCV) infections. The viral proteases (HIV protease and HCV NS3/4A protease) are primary drug targets. At the molecular level, drug resistance reflects a subtle change in the balance of molecular recognition; the drug resistant protease variants are no longer effectively inhibited by the competitive drug molecules but can process the natural substrates with enough efficiency for viral survival. Therefore, the inhibitors that better mimic the natural substrate binding features should result in more robust inhibitors with flat drug resistance profiles. The native substrates adopt a consensus volume when bound to the enzyme, the substrate envelope. The most severe resistance mutations occur at protease residues that are contacted by the inhibitors outside the substrate envelope. To guide the design of robust inhibitors, we investigate the shared and varied properties of substrates with the protein dynamics taken into account to define the dynamic substrate envelope of both viral proteases. The NS3/4A dynamic substrate envelope is compared with inhibitors to detect the structural and dynamic basis of resistance mutation patterns. Comparative analyses of substrates and inhibitors result in a solid list of structural and dynamic features of substrates that are not shared by inhibitors. This study can help guiding the development of novel inhibitors by paying attention to the subtle differences between the binding properties of substrates versus inhibitors.
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Ozen, Aysegul. "Structure and Dynamics of Viral Substrate Recognition and Drug Resistance: A Dissertation." eScholarship@UMMS, 2005. http://escholarship.umassmed.edu/gsbs_diss/677.

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Drug resistance is a major problem in quickly evolving diseases, including the human immunodeficiency (HIV) and hepatitis C viral (HCV) infections. The viral proteases (HIV protease and HCV NS3/4A protease) are primary drug targets. At the molecular level, drug resistance reflects a subtle change in the balance of molecular recognition; the drug resistant protease variants are no longer effectively inhibited by the competitive drug molecules but can process the natural substrates with enough efficiency for viral survival. Therefore, the inhibitors that better mimic the natural substrate binding features should result in more robust inhibitors with flat drug resistance profiles. The native substrates adopt a consensus volume when bound to the enzyme, the substrate envelope. The most severe resistance mutations occur at protease residues that are contacted by the inhibitors outside the substrate envelope. To guide the design of robust inhibitors, we investigate the shared and varied properties of substrates with the protein dynamics taken into account to define the dynamic substrate envelope of both viral proteases. The NS3/4A dynamic substrate envelope is compared with inhibitors to detect the structural and dynamic basis of resistance mutation patterns. Comparative analyses of substrates and inhibitors result in a solid list of structural and dynamic features of substrates that are not shared by inhibitors. This study can help guiding the development of novel inhibitors by paying attention to the subtle differences between the binding properties of substrates versus inhibitors.
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Sala, Davide. "Application of molecular dynamics to the understanding of metal-binding macromolecules and their adducts." Doctoral thesis, 2019. http://hdl.handle.net/2158/1179863.

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Reddy, Tyler. "Structure, Flexibility, And Overall Motion Of Transmembrane Peptides Studied By NMR Spectroscopy And Molecular Dynamics Simulations." 2011. http://hdl.handle.net/10222/15719.

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Nuclear magnetic resonance (NMR) spectroscopy was used to determine the structure of transmembrane (TM) segment IX of the Na+/H+ exchanger isoform 1 (NHE1) in dodecylphosphocholine micelles. Studying isolated TM segments in this fashion constitutes a well-established "divide and conquer" approach to the study of membrane proteins, which are often extremely difficult to produce, purify, and reconstitute in full-length polytopic form. A similar approach was combined with NMR spin relaxation experiments to determine the peptide backbone flexibility of NHE1 TM VII. The combined NMR structural and dynamics studies are consistent with an important role for TM segment flexibility in the function of NHE1, a protein involved in apoptosis and myocardial disease. The study of the rhomboid protease system is also described from two perspectives: 1) I attempted to produce several TM constructs of the substrate spitz or a related construct and the production and purification are described in detail; and 2) I present coarse-grained molecular dynamics simulation results for the E. coli rhomboid ecGlpG and a spitz TM construct. Spitz appears to preferentially associate with rhomboid near TMs 1 and 3 rather than the proposed substrate gate at TM 5. The two proteins primarily interact at the termini of helices rather than within the hydrocarbon core of the bilayer. Finally, I present a detailed analysis of coarse-grained molecular dynamics simulations of the fibroblast growth factor receptor 3 TM domain dimerization. Specifically, algorithms are described for analyzing critical features of wild-type and G380R mutant constructs. The G380R mutation is the cause of achondroplasia, the most common form of human dwarfism. The results suggest that the proximity of a residue to the dimer interface may impact the severity of the mutant phenotype. Strikingly, heterodimer and mutant homodimer constructs exhibit a secondary dimer interface which may explain the increased signaling activity previously reported for the G380R mutation--the helices may rotate with the introduction of G380R. The unifying theme of this work is the 'study of membrane proteins' using complementary techniques from structural biology and computational biochemistry.
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Books on the topic "Molecular dynamics, metalloproteins, structural biology, proteins structure"

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Rupp, Bernhard. Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology. CRC Press LLC, 2009.

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Book chapters on the topic "Molecular dynamics, metalloproteins, structural biology, proteins structure"

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Saibo, Nikita V., Snigdha Maiti, Bidisha Acharya, and Soumya De. "Analysis of structure and dynamics of intrinsically disordered regions in proteins using solution NMR methods." In Advances in Protein Molecular and Structural Biology Methods, 535–50. Elsevier, 2022. http://dx.doi.org/10.1016/b978-0-323-90264-9.00032-5.

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Opella, Stanley J. "The Roles of Structure, Dynamics and Assembly in the Display of Peptides on Filamentous Bacteriophage." In Phage Nanobiotechnology, 12–32. The Royal Society of Chemistry, 2011. http://dx.doi.org/10.1039/bk9780854041848-00012.

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The filamentous bacteriophages are extraordinarily interesting biological organisms in their own right with a fascinating lifecycle that involves the host cell membrane even though they do not possess a membrane themselves. With the ability to accept additional nucleotides they have proven to be among the most useful tools in experimental molecular biology and biotechnology. The structures of the coat proteins of both Class I (fd) and Class II (Pf1) bacteriophages in both their membrane-bound and structural forms in the bacteriophage particles demonstrate fundamental complexity in the structure and dynamics of apparently small helical proteins. The structures or the end points enable a model of the assembly process to be developed. And all of this structural information informs the design and expression of peptides displayed on the surface of bacteriophages, which is one of the principal applications of these systems in biomedical and biotechnological research.
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Silva, Cândida G., Pedro Gabriel Ferreira, Paulo J. Azevedo, and Rui M. M. Brito. "Using Data Mining Techniques to Probe the Role of Hydrophobic Residues in Protein Folding and Unfolding Simulations." In Evolving Application Domains of Data Warehousing and Mining, 258–76. IGI Global, 2010. http://dx.doi.org/10.4018/978-1-60566-816-1.ch012.

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The protein folding problem, i.e. the identification of the rules that determine the acquisition of the native, functional, three-dimensional structure of a protein from its linear sequence of amino-acids, still is a major challenge in structural molecular biology. Moreover, the identification of a series of neurodegenerative diseases as protein unfolding/misfolding disorders highlights the importance of a detailed characterisation of the molecular events driving the unfolding and misfolding processes in proteins. One way of exploring these processes is through the use of molecular dynamics simulations. The analysis and comparison of the enormous amount of data generated by multiple protein folding or unfolding simulations is not a trivial task, presenting many interesting challenges to the data mining community. Considering the central role of the hydrophobic effect in protein folding, we show here the application of two data mining methods – hierarchical clustering and association rules – for the analysis and comparison of the solvent accessible surface area (SASA) variation profiles of each one of the 127 amino-acid residues in the amyloidogenic protein Transthyretin, across multiple molecular dynamics protein unfolding simulations.
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