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Academic literature on the topic 'Conformation Dynamics'

Author: Grafiati

Published: 7 September 2023

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Journal articles on the topic "Conformation Dynamics"

1

Ohno, Shiho, Noriyoshi Manabe, Takumi Yamaguchi, Jun Uzawa, and Yoshiki Yamaguchi. "Ribitol in Solution Is an Equilibrium of Asymmetric Conformations." Molecules 26, no. 18 (September 8, 2021): 5471. http://dx.doi.org/10.3390/molecules26185471.

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Ribitol (C5H12O5), an acyclic sugar alcohol, is present on mammalian α-dystroglycan as a component of O-mannose glycan. In this study, we examine the conformation and dynamics of ribitol by database analysis, experiments, and computational methods. Database analysis reveals that the anti-conformation (180°) is populated at the C3–C4 dihedral angle, while the gauche conformation (±60°) is seen at the C2–C3 dihedral angle. Such conformational asymmetry was born out in a solid-state 13C-NMR spectrum of crystalline ribitol, where C1 and C5 signals are unequal. On the other hand, solution 13C-NMR has identical chemical shifts for C1 and C5. NMR 3J coupling constants and OH exchange rates suggest that ribitol is an equilibrium of conformations, under the influence of hydrogen bonds and/or steric hinderance. Molecular dynamics (MD) simulations allowed us to discuss such a chemically symmetric molecule, pinpointing the presence of asymmetric conformations evidenced by the presence of correlations between C2–C3 and C3–C4 dihedral angles. These findings provide a basis for understanding the dynamic structure of ribitol and the function of ribitol-binding enzymes.

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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.

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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.

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Qu, Kun, Qiuluan Chen, Katarzyna A. Ciazynska, Banghui Liu, Xixi Zhang, Jingjing Wang, Yujie He, et al. "Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike." PLOS Pathogens 18, no. 7 (July 29, 2022): e1010583. http://dx.doi.org/10.1371/journal.ppat.1010583.

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The spike (S) protein of SARS-CoV-2 has been observed in three distinct pre-fusion conformations: locked, closed and open. Of these, the function of the locked conformation remains poorly understood. Here we engineered a SARS-CoV-2 S protein construct “S-R/x3” to arrest SARS-CoV-2 spikes in the locked conformation by a disulfide bond. Using this construct we determined high-resolution structures confirming that the x3 disulfide bond has the ability to stabilize the otherwise transient locked conformations. Structural analyses reveal that wild-type SARS-CoV-2 spike can adopt two distinct locked-1 and locked-2 conformations. For the D614G spike, based on which all variants of concern were evolved, only the locked-2 conformation was observed. Analysis of the structures suggests that rigidified domain D in the locked conformations interacts with the hinge to domain C and thereby restrains RBD movement. Structural change in domain D correlates with spike conformational change. We propose that the locked-1 and locked-2 conformations of S are present in the acidic high-lipid cellular compartments during virus assembly and egress. In this model, release of the virion into the neutral pH extracellular space would favour transition to the closed or open conformations. The dynamics of this transition can be altered by mutations that modulate domain D structure, as is the case for the D614G mutation, leading to changes in viral fitness. The S-R/x3 construct provides a tool for the further structural and functional characterization of the locked conformations of S, as well as how sequence changes might alter S assembly and regulation of receptor binding domain dynamics.

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Guo, Qing, Yufan He, and H. Peter Lu. "Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy." Proceedings of the National Academy of Sciences 112, no. 45 (October 28, 2015): 13904–9. http://dx.doi.org/10.1073/pnas.1506405112.

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Characterizing the impact of fluctuating enzyme conformation on enzymatic activity is critical in understanding the structure–function relationship and enzymatic reaction dynamics. Different from studying enzyme conformations under a denaturing condition, it is highly informative to manipulate the conformation of an enzyme under an enzymatic reaction condition while monitoring the real-time enzymatic activity changes simultaneously. By perturbing conformation of horseradish peroxidase (HRP) molecules using our home-developed single-molecule total internal reflection magnetic tweezers, we successfully manipulated the enzymatic conformation and probed the enzymatic activity changes of HRP in a catalyzed H2O2–amplex red reaction. We also observed a significant tolerance of the enzyme activity to the enzyme conformational perturbation. Our results provide a further understanding of the relation between enzyme behavior and enzymatic conformational fluctuation, enzyme–substrate interactions, enzyme–substrate active complex formation, and protein folding–binding interactions.

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Ludwiczak, Jan, Ewa Szczęsna, Antônio Marinho da Silva Neto, Piotr Cieplak, Andrzej A. Kasprzak, and Adam Jarmuła. "Interactions between motor domains in kinesin-14 Ncd — a molecular dynamics study." Biochemical Journal 476, no. 17 (September 10, 2019): 2449–62. http://dx.doi.org/10.1042/bcj20190484.

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Abstract Minus-end directed, non-processive kinesin-14 Ncd is a dimeric protein with C-terminally located motor domains (heads). Generation of the power-stroke by Ncd consists of a lever-like rotation of a long superhelical ‘stalk’ segment while one of the kinesin's heads is bound to the microtubule. The last ∼30 amino acids of Ncd head play a crucial but still poorly understood role in this process. Here, we used accelerated molecular dynamics simulations to explore the conformational dynamics of several systems built upon two crystal structures of Ncd, the asymmetrical T436S mutant in pre-stroke/post-stroke conformations of two partner subunits and the symmetrical wild-type protein in pre-stroke conformation of both subunits. The results revealed a new conformational state forming following the inward motion of the subunits and stabilized with several hydrogen bonds to residues located on the border or within the C-terminal linker, i.e. a modeled extension of the C-terminus by residues 675–683. Forming of this new, compact Ncd conformation critically depends on the length of the C-terminus extending to at least residue 681. Moreover, the associative motion leading to the compact conformation is accompanied by a partial lateral rotation of the stalk. We propose that the stable compact conformation of Ncd may represent an initial state of the working stroke.

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Bierzyński, A. "Methods of peptide conformation studies." Acta Biochimica Polonica 48, no. 4 (December 31, 2001): 1091–99. http://dx.doi.org/10.18388/abp.2001_3870.

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In solution most of the peptides assume multiple flexible conformations. Determination of the dominant conformers and evaluation of their populations is the aim of peptide conformation studies, in which theoretical and experimental methods play complementary roles. Molecular dynamics or Monte Carlo methods are quite effective in searching the conformational space accessible to a peptide but they are not able to estimate, precisely enough, the populations of various conformations. Therefore, they must be supplemented by experimental data. In this paper, a short review of the experimental methods, most widely used in peptide conformational studies, is presented. Among them NMR plays the leading role. Valuable information is also obtained from hydrogen exchange, fluorescence resonance energy transfer, and circular dichroism measurements. The advantages and shortcomings of these methods are discussed.

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Gaalswyk, Kari, and Christopher N. Rowley. "An explicit-solvent conformation search method using open software." PeerJ 4 (May 31, 2016): e2088. http://dx.doi.org/10.7717/peerj.2088.

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Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the gas phase or with an implicit solvent model. We have developed a work-flow for performing a conformation search on explicitly-solvated molecules using open source software. This method uses replica exchange molecular dynamics (REMD) to sample the conformational states of the molecule efficiently. Cluster analysis is used to identify the most probable conformations from the simulated trajectory. This work-flow was tested on drug molecules α-amanitin and cabergoline to illustrate its capabilities and effectiveness. The preferred conformations of these molecules in gas phase, implicit solvent, and explicit solvent are significantly different.

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Lin, Shawn H., Dacheng Zhao, Vivian Deng, Veronica K. Birdsall, Suzanne Ho, Olga Buzovetsky, Candice M. Etson, and Ishita Mukerji. "Integration Host Factor Binds DNA Holliday Junctions." International Journal of Molecular Sciences 24, no. 1 (December 29, 2022): 580. http://dx.doi.org/10.3390/ijms24010580.

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Integration host factor (IHF) is a nucleoid-associated protein involved in DNA packaging, integration of viral DNA and recombination. IHF binds with nanomolar affinity to duplex DNA containing a 13 bp consensus sequence, inducing a bend of ~160° upon binding. We determined that IHF binds to DNA Four-way or Holliday junctions (HJ) with high affinity regardless of the presence of the consensus sequence, signifying a structure-based mechanism of recognition. Junctions, important intermediates in DNA repair and homologous recombination, are dynamic and can adopt either an open or stacked conformation, where the open conformation facilitates branch migration and strand exchange. Using ensemble and single molecule Förster resonance energy transfer (FRET) methods, we investigated IHF-induced changes in the population distribution of junction conformations and determined that IHF binding shifts the population to the open conformation. Further analysis of smFRET dynamics revealed that even in the presence of protein, the junctions remain dynamic as fast transitions are observed for the protein-bound open state. Protein binding alters junction conformational dynamics, as cross correlation analyses reveal the protein slows the transition rate at 1 mM Mg2+ but accelerates the transition rate at 10 mM Mg2+. Stopped flow kinetic experiments provide evidence for two binding steps, a rapid, initial binding step followed by a slower step potentially associated with a conformational change. These measurements also confirm that the protein remains bound to the junction during the conformer transitions and further suggest that the protein forms a partially dissociated state that allows junction arms to be dynamic. These findings, which demonstrate that IHF binds HJs with high affinity and stabilizes junctions in the open conformation, suggest that IHF may play multiple roles in the processes of integration and recombination in addition to stabilizing bacterial biofilms.

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Mizutani, Tadashi, and Shigeyuki Yagi. "Linear tetrapyrroles as functional pigments in chemistry and biology." Journal of Porphyrins and Phthalocyanines 08, no. 03 (March 2004): 226–37. http://dx.doi.org/10.1142/s1088424604000210.

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1,19,21,24-tetrahydro-1,19-bilindione is the framework of pigments frequently found in nature, which includes biliverdin IX α, phytochromobilin and phycocyanobilin. 1,19-bilindiones have unique features such as (1) photochemical and thermal cis-trans isomerization, (2) excited energy transfer, (3) chiroptical properties due to the cyclic helical conformation, (4) redox activity, (5) coordination to various metals, and (6) reconstitution to proteins. 1,19-bilindione can adopt a number of conformations since it has exocyclic three double bonds and three single bonds that are rotatable thermally and photochemically. In solution, biliverdin and phycocyanobilin adopt a cyclic helical ZZZ, syn, syn, syn conformation, but other conformations are stabilized depending on the experimental conditions and substituents on the bilin framework. The conformational changes in 1,19-bilindiones are related to the biological functions of a photoreceptor protein, phytochrome. Structural and conformational studies of bilindiones are summarized both in solution and in protein. The conformational changes of bilins can be used for other functions such as a chirality sensor. The bilindiones and the zinc complexes of bilindiones can be employed as a chirality sensor due to the helically chiral structure and the dynamics of racemization of enantiomers. In this paper, we discuss the conformational equilibria and dynamics of bilindiones and its implications in photobiology and materials science.

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Verma, Rajni, Jonathan M. Ellis, and Katie R. Mitchell-Koch. "Dynamic Preference for NADP/H Cofactor Binding/Release in E. coli YqhD Oxidoreductase." Molecules 26, no. 2 (January 7, 2021): 270. http://dx.doi.org/10.3390/molecules26020270.

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YqhD, an E. coli alcohol/aldehyde oxidoreductase, is an enzyme able to produce valuable bio-renewable fuels and fine chemicals from a broad range of starting materials. Herein, we report the first computational solution-phase structure-dynamics analysis of YqhD, shedding light on the effect of oxidized and reduced NADP/H cofactor binding on the conformational dynamics of the biocatalyst using molecular dynamics (MD) simulations. The cofactor oxidation states mainly influence the interdomain cleft region conformations of the YqhD monomers, involved in intricate cofactor binding and release. The ensemble of NADPH-bound monomers has a narrower average interdomain space resulting in more hydrogen bonds and rigid cofactor binding. NADP-bound YqhD fluctuates between open and closed conformations, while it was observed that NADPH-bound YqhD had slower opening/closing dynamics of the cofactor-binding cleft. In the light of enzyme kinetics and structural data, simulation findings have led us to postulate that the frequently sampled open conformation of the cofactor binding cleft with NADP leads to the more facile release of NADP while increased closed conformation sampling during NADPH binding enhances cofactor binding affinity and the aldehyde reductase activity of the enzyme.

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Dissertations / Theses on the topic "Conformation Dynamics"

1

Link, Justin J. "Ultrafast Protein Conformation Dynamics." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1230584570.

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Zang, Chen. "Ultrafast Spectroscopic Study of Protein Conformation Dynamics and Hydration Dynamics." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1299481658.

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Zhang, Lyndon N. (Lyndon Nuoxi). "Conformation and dynamics of the mammalian chromosome." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/103441.

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Thesis: S.M., Massachusetts Institute of Technology, Department of Biology, 2016.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 29-30).
The control of transcription represents a fundamental, initial mechanism by which the regulation of gene expression is implemented. However, while much research has been done on the biochemistry and cellular function of transcription, comparatively little is known on the dynamics of transcriptional mechanisms, their impact on chromatin structure, and concomitant functional consequences. Employing chromatin immunoprecipitation measurements, we report progress towards this goal. We characterize the ensemble chromosome conformation in mouse embryonic stem cells, by measuring interaction, or contact, probabilities between distal genomic loci. We map and describe chromosome loops, consisting of two interacting CTCF sites co-bound by cohesin, that maintain the expression of genes known to promote cell identity, and restrict the expression of genes specifying repressed developmental lineages.
by Lyndon N. Zhang.
S.M.

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4

Wooten, E. Wrenn. "Structure, conformation and dynamics of N-linked oligosaccharides." Thesis, University of Oxford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.253421.

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Winsborrow, BeAtrice G. "Glycolipid conformation and dynamics in model and biological membranes." Thesis, University of Ottawa (Canada), 1993. http://hdl.handle.net/10393/6811.

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The focus of this dissertation has been the biophysical analysis of two related research subjects: a model membrane glycolipid system and glycolipid-rich biomembranes. The objective of the model system study was to provide a biological understanding of the molecular conformation and dynamics at the membrane surface. The biomembrane project is in the first stages of development where the immediate goal is to observe the structure and phase behaviour of cyanobacterial thylakoid membranes. It has been possible to apply a motional model deduced for the glycerol C3$\sp\prime$ position of 1,2-di-O-tetradecyl-3-O-$(\beta$-D-glucopyranosyl)-sn-glycerol $(\beta$-DTGL) in the gel state not only to the more fluid liquid crystalline state, but also to the analysis of the glucose head group ($\{$1-$\rm \sp2H\sb1\})$ motions. The above model, however, did not completely simulate the relaxation data of the $\beta$-DTGL glucose head group. Therefore, conformational energy calculations have been used to assess the flexibility of the head group about its glycosidic bond, in a liquid-crystalline membrane matrix. Algal thylakoid membranes are known for their ability to undergo conformational changes during periods of photosynthetic activity. The ultimate goal of the biomembrane project was to use $\sp2$H NMR to study such conformational changes in thylakoid membranes. However, this project is in the first stages of development; the more modest but attainable short term goal was to observe directly the structure and phase behaviour of two strains of cyanobacterial thylakoid membranes, Anacystis nidulans and A. nidulans R2. In both the previous studies and this study, it was found that the heterogeneous systems undergo broad phase transitions and that acyl chain unsaturation lowers the phase transition temperature of the membranes. Although pure digalactosyldiacyglycerol is known to stabilize lamellar membrane phases, it appears as though phosphatidylglycerol (PG) is more influential in stabilizing the lamellar membrane structure of the cyanobacterial thylakoid membranes. This effect was more noticeable for the spectra of extracted lipids; in the absence of protein and with low PG levels, the lipids formed non-lamellar phases at lower temperatures. (Abstract shortened by UMI.)

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6

Qian, Hong. "Conformation and dynamics of main-chain liquid crystalline polymers." Thesis, Heriot-Watt University, 2004. http://hdl.handle.net/10399/245.

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7

Dauber-Osguthorpe, Pnina. "Conformation and internal motion of polypeptides : molecular dynamics simulations." Thesis, University of Bath, 1990. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.252972.

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8

Mcgeagh, John David. "Conformation and cooperativity in homodimeric enzymes investigated by molecular dynamics simulations." Thesis, University of Bristol, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.549446.

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9

Mark, Pekka. "Molecular dynamics studies of water and biomolecules /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-251-5.

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10

Rönnols, Jerk. "Structure, dynamics and reactivity of carbohydrates : NMR spectroscopic studies." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-92408.

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The main focus of this thesis is on the ring conformations of carbohydrate molecules; how the conformational equilibria and the rates of the associated interconversions are affected by the molecular constitution and their surroundings. The conformational equilibria of a group of amine linked pseudodisaccharides, designed as potential glycosidase inhibitors, comprising α-D-altrosides are described in Chapter 3. The OS2 conformation was largely populated, and the ring conformation was found to depend on the charge of the amine functionality. The conformations of β-D-xylopyranoside derivatives with naphthyl-based aglycones, which are potential anti-cancer agents, are described in chapter 4. Solvent dependent flexibility was observed. Intramolecular hydrogen bonds were concluded to be involved in the stabilization of 1C4 conformers in non-hydrogen bonding solvents of low polarity. Chapter 5 describes the first measurements of the conformational exchange rates of mannuronic acid ester derivatives between the 4C1 and 1C4 conformations, through DNMR measurements. The relative reactivity of glycosyl triflates as electrophiles in glycosylation reactions were investigated with NMR-based competition experiments. In Chapter 6, investigations of ruthenium-catalyzed epimerizations of the allylic alcohols of glycal derivatives, and stereoselective synthesis of esters through a DYKAT protocol, are described. The kinetics of the epimerizations were elaborated through different NMR-spectroscopic methods. Chapter 7 describes additions of NMR chemical shift data of mono- and oligosaccharides to database of the computer program CASPER, and applications thereof.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 5: Manuscript.

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Books on the topic "Conformation Dynamics"

1

Weber, Marcus. Meshless methods in conformation dynamics. München: Hut, 2006.

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Mitsuru, Nagasawa, Kurata Michio 1925-, and Toyota Conference, (1st : 1987 : Inuyama City,Japan), eds. Molecular conformation and dynamics of macromolecules in condensed systems. Amsterdam: Elsevier, 1988.

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A, Winnik Mitchell, and North Atlantic Treaty Organization. Scientific Affairs Division., eds. Photophysical and photochemical tools in polymer science: Conformation, dynamics, morphology. Dordrecht: D. Reidel Pub. Co., 1986.

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Subbiah, S. Protein motions. New York: Chaoman & Hall, 1996.

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Livesay, Dennis R. Protein dynamics: Methods and protocols. New York: Humana Press, 2013.

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6

Course on Dynamics and the Problem of Recognition in Biological Macromolecules (2nd 1995 Erice, Italy). Dynamics and the problem of recognition in biological macromolecules. New York: Plenum Press, 1996.

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Toyota Conference (1st 1987 Inuyama-shi, Japan). Molecular conformation and dynamics of macromolecules in condensed systems: A collection of contributions based on lectures presented at the 1st Toyota Conference, Inuyama City, Japan, 28 September-1 October 1987. Amsterdam: Elsevier, 1988.

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International Symposium on Structure and Dynamics of Nucleic Acids, Proteins, and Membranes (1986 Riva, Italy). Structure and dynamics of nucleic acids, proteins, and membranes. New York: Plenum Press, 1986.

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9

Han, Ke-li, Xin Zhang, and Ming-jun Yang, eds. Protein Conformational Dynamics. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-02970-2.

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Keresü, G. M. Molecular mechanics and conformational analysis in drug design. Oxford: Blackwell Science, 1999.

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Book chapters on the topic "Conformation Dynamics"

1

Brogaard, Rasmus Y. "Aspects and Investigation of Photochemical Dynamics." In Molecular Conformation and Organic Photochemistry, 7–21. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-29381-8_2.

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Tsou, C. L. "Conformation and Dynamics of Oligomeric Enzymes." In Enzyme Dynamics and Regulation, 342–50. New York, NY: Springer New York, 1988. http://dx.doi.org/10.1007/978-1-4612-3744-0_39.

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Brogaard, Rasmus Y. "Probing Structural Dynamics by Interaction Between Chromophores." In Molecular Conformation and Organic Photochemistry, 103–14. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-29381-8_9.

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Deuflhard, Peter. "From Molecular Dynamics to Conformation Dynamics in Drug Design." In Trends in Nonlinear Analysis, 269–87. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05281-5_6.

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Khokhlov, Alexei R., Victor A. Ivanov, Alexander V. Chertovich, Alexei A. Lazutin, and Pavel G. Khalatur. "Conformation-Dependent Sequence Design of Copolymers." In Structure and Dynamics of Confined Polymers, 333–50. Dordrecht: Springer Netherlands, 2002. http://dx.doi.org/10.1007/978-94-010-0401-5_21.

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Vallee, Bert L., and James F. Riordan. "Dynamics of Local Conformation and Enzyme Function." In Novartis Foundation Symposia, 197–223. Chichester, UK: John Wiley & Sons, Ltd., 2008. http://dx.doi.org/10.1002/9780470720424.ch12.

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Gibbons, W. A., P. Mascagni, N. Zhou, A. E. Aulabaugh, A. Prugnola, M. Kuo, and N. Niccolai. "The Role of Conformation and Conformational Dynamics in Biological Information Transfer." In Advanced Magnetic Resonance Techniques in Systems of High Molecular Complexity, 77–88. Boston, MA: Birkhäuser Boston, 1986. http://dx.doi.org/10.1007/978-1-4615-8521-3_7.

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Gherardi, Marco, Vittore Scolari, Remus Thei Dame, and Marco Cosentino Lagomarsino. "Chromosome Structure and Dynamics in Bacteria: Theory and Experiments." In Modeling the 3D Conformation of Genomes, 207–30. Boca Raton : Taylor & Francis, 2018. | Series: Series in computational biophysics ; 4: CRC Press, 2019. http://dx.doi.org/10.1201/9781315144009-9.

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Awasthi, Nidhi, Rohit Shukla, Devesh Kumar, Arvind Kumar Tiwari, and Timir Tripathi. "Monte Carlo Approaches to Study Protein Conformation Ensembles." In Protein Folding Dynamics and Stability, 129–46. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-2079-2_7.

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Amitai, A., and D. Holcman. "Analysis of Chromatin Dynamics and Search Processes in the Nucleus." In Modeling the 3D Conformation of Genomes, 177–206. Boca Raton : Taylor & Francis, 2018. | Series: Series in computational biophysics ; 4: CRC Press, 2019. http://dx.doi.org/10.1201/9781315144009-8.

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Conference papers on the topic "Conformation Dynamics"

1

Golodnizky, Daniel, Carlos E. S. Bernardes, Maya Davidovich-Pinhas, Ronit Bitton, and Yulia Shmidov. "Isotropic liquid state of triacylglycerols: The starting point of fats and oils crystallization." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/ggfh1118.

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Over the years, several models of triacylglycerol (TAG) molecular conformations and bulk arrangements in isotropic liquid state have been proposed and are still up for debate. This organization is the starting state, from which the molecules self-assemble and form the initial stable nucleus, which then grows to form the solid crystal. The current research aims to explore the isotropic liquid state, while focusing on its impact on nucleation and crystal formation. This aim was addressed by implementing experimental methods, such as X-ray diffraction and small-angle X-ray scattering coupled with a computational method, such as molecular dynamics simulation. These techniques were used to study tristearin and triolein as models for saturated and unsaturated TAGs, respectively. Four different conformations were suggested for the two TAGs, and the results showed conformation abundancy in the order: trident (Tr) > chair (Ch) > propeller (Pr) > tuning-fork (Tf). The existence of clusters was demonstrated, each of which exhibited a heterogeneous distribution of conformations. The preferability to find a specific pair of conformations next to each other was analyzed and, surprisingly, it was found that Tf will preferably pair only with Tr although Tf is the preferable conformation in most crystal polymorphs. High general conversion rates from any conformation to another, and high specific conversion rates from and to the Tf conformation were calculated. It is proposed that the high conversion rates observed enable the crystallization process, despite the low proportion of Tf molecules. Overall, the results confirm the formation of specific structures in the liquid state, which combine all previously suggested models and further expand the knowledge using experimental and computational tools.

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2

Karplus, M. "Internal dynamics of macromolecules : Simulations of motion in proteins." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.thb1.

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The internal motions of proteins will be discussed. Detailed atom-bases simulations of the native conformation space will be supplemented by simplified models for the full conformation space involved in protein folding.

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Nakayama, H. "Structure and Relaxation of Amorphous Molecular Systems Studied by Transformation between Conformation Isomers." In FLOW DYNAMICS: The Second International Conference on Flow Dynamics. AIP, 2006. http://dx.doi.org/10.1063/1.2204480.

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Maghsoodi, Ameneh, Anupam Chatterjee, Ioan Andricioaei, and Noel Perkins. "An Approximate Model of the Dynamics of the Bacteriophage T4 Injection Machinery." In ASME 2016 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/detc2016-60281.

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Bacteriophage T4 is one of the most common and complex of the tailed viruses that infect host bacteria using an intriguing contractile tail assembly. Despite extensive progress in resolving the structure of T4, the dynamics of the injection machinery remains largely unknown. This paper contributes a first model of the injection machinery that is driven by elastic energy stored in a structure known as the sheath. The sheath is composed of helical strands of protein that suddenly collapse from an energetic, extended conformation prior to infection to a relaxed, contracted conformation during infection. We employ Kirchhoff rod theory to simulate the nonlinear dynamics of a single protein strand coupled to a model for the remainder of the virus, including the coupled translation and rotation of the head (capsid), neck and tail tube. Doing so provides an important building block towards the future goal of modeling the entire sheath structure which is composed of six interacting helical protein strands. The resulting numerical model exposes fundamental features of the injection machinery including the time scale and energetics of the infection process, the nonlinear conformational change experienced by the sheath, and the contribution of hydrodynamic drag on the head (capsid).

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Kabir, Kazi Lutful, Ruth Nussinov, Buyong Ma, and Amarda Shehu. "Antigen Binding Reshapes Antibody Energy Landscape and Conformation Dynamics." In 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2021. http://dx.doi.org/10.1109/bibm52615.2021.9669830.

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Lim, Manko, Timothy A. Jackson, and Philip A. Anfinrud. "Ultrafast Near-IR Spectroscopy of Carbonmonoxymyoglobin: the Dynamics of Protein Relaxation." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.thb3.

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The conformation of a protein often influences its activity, yielding a structure-function relationship. X-ray diffraction studies have shown that the tertiary structures of ligated and deligated myoglobin (Mb) are somewhat different1. Consequently, dissociation of a ligand from Mb triggers a transition between the two tertiary conformations. The potential energy gradient causing this change is developed at the heme; the iron prefers to be in the plane of the porphyrin in ligated Mb but is displaced 0.5 Å from the plane of the porphyrin in deoxy Mb. The dynamics of this conformational transition may influence the dynamics of rebinding ligands, implying that protein dynamics are also functionally important. For example, the dynamics of ligand recombination with Mb following photolysis of MbCO or MbO2 in low-temperature glasses are similar2. In contrast, Mb expurgates CO with far greater efficiency than O2 when photolysis is carried out at biologically important temperatures3. Since protein motion is inhibited at low temperatures, protein relaxation likely accounts for the temperature-dependent difference in the quantum yield of photodissociation. The ability to discriminate against the binding and storage of CO is functionally important as endogenously produced CO would otherwise compete effectively with O2 for binding sites. A steric mechanism for discriminating against the binding of CO, involving the distal histidine, is well known. The dynamics of protein relaxation evidently provide a mechanism for discriminating against the storage of CO. We have investigated the dynamics of protein relaxation in order to probe this mechanism and thereby elucidate the relation between protein dynamics and function.

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Bidone, Tamara C., Marco A. Deriu, Giacomo Di Benedetto, Diana Massai, and Umberto Morbiducci. "Insights Into the Molecular Mechanisms of Actin Dynamics: A Multiscale Modeling Approach." In ASME 2011 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2011. http://dx.doi.org/10.1115/sbc2011-53417.

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Actin dynamics, which is at the basis of many fundamental cellular processes as cell migration [1], is governed by the self-assembly and disassembly of actin monomers (G-actin) that, in turn, are determined by the kinetics of ATP hydrolysis and by the local concentrations of Mg2+ and Ca2+ [2]. During cell migration, interactions of the actin filaments (F-actin) with different nucleotide-cation complexes induce local topological rearrangements, because the filament building G-actins undergo conformational shifts between multiple equilibrium states separated by low-energy barriers. For example, the structural rearrangements of the DNase-I binding loop (residues 38–52) in subdomain 2 are driven by ATP hydrolysis and the changes in the conformation of subdomain 4 are induced by the presence of a tightly-bound Mg2+ or Ca2+ ion (Figure 1a). These conformational shifts alter the cross-linking between monomers, varying the contact surfaces among adjacent inter- and intrasubdomains of G-actin, and reflect on the overall properties of F-actin.

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Philips, Laura A., Christopher L. Brummel, and Steven W. Mork. "High resolution infrared spectroscopy as a tool to measure chemical reaction dynamics." In OSA Annual Meeting. Washington, D.C.: Optica Publishing Group, 1991. http://dx.doi.org/10.1364/oam.1991.thq4.

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Both intra- and intermolecular interactions play an important role in determining the potential surface for a chemical reaction. Such interactions determine both physical structure and chemical reactivity. High resolution infrared spectroscopy has been used to probe both molecular structure and vibrationally induced chemistry. 2-fluorethanol is an example of a molecule in which the strong attractive interactions between F and the OH moity not only determine the lowest energy conformation of the molecule, but also the most efficient vibrational excitation for inducing conformational isomerization. An analogue of 2-fluoroethanol, 1,2-difluoroethane, although similar in structure, has quite different intramolecular interactions. These differences are apparent in both the isomerization dynamics and the spectroscopy. Spectra were measured using a color center laser with optothermal detection (resolution = 10-4 cm-1). The spectra of these molecules allow us to link vibrational mode-coupling to chemical reactivity.

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Lin, Tu-Liang, and Guang Song. "Generalized spring tensor models for protein fluctuation dynamics and conformation changes." In 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshop, BIBMW. IEEE, 2009. http://dx.doi.org/10.1109/bibmw.2009.5332117.

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Davis, John, and Nathanael Kidwell. "CONFORMATION-SPECIFIC INSIGHTS INTO THE CHEMICAL DYNAMICS OF NO:CH4 MOLECULAR COMPLEXES." In 2022 International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2022. http://dx.doi.org/10.15278/isms.2022.wa06.

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Reports on the topic "Conformation Dynamics"

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Schaufele, Fred. Temporal and Spatial Dynamics of Androgen Receptor Conformation and Interactions in Prostate Cancer Cells. Fort Belvoir, VA: Defense Technical Information Center, November 2007. http://dx.doi.org/10.21236/ada477345.

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Schutt, Timothy C., and Manoj K. Shukla. Computational Investigation on Interactions Between Some Munitions Compounds and Humic Substances. Engineer Research and Development Center (U.S.), February 2021. http://dx.doi.org/10.21079/11681/39703.

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Humic acid substances (HAs) in natural soil and sediment environments effect the retention and degradation of insensitive munitions compounds and legacy high explosives (MCs): DNAN, DNi- NH4+, nMNA, NQ, NTO (neutral and anionic forms), TNT, and RDX.A humic acid model compound has been considered using molecular dynamics, thermodynamic integration, and density functional theory to characterize the munition binding ability, ionization potential, and electron affinity compared to that in the water solution. Humic acids bind most compounds and act as both a sink and source for electrons. Ionization potentials suggest HAs are more susceptible to oxidation than the MCs studied. The electron affinity of HAs are very conformation-dependent and spans the same range as the munition compounds. When HAs and MCs are complexed the HAs tend to radicalize first thus buffering MCs against reductive as well as oxidative attacks.

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Hanke, Andreas. Studies of Single Biomolecules, DNA Conformational Dynamics, and Protein Binding. Fort Belvoir, VA: Defense Technical Information Center, July 2008. http://dx.doi.org/10.21236/ada483440.

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Laurence, Ted Alfred. Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions. Office of Scientific and Technical Information (OSTI), January 2002. http://dx.doi.org/10.2172/813378.

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Hong, Mei. Two-dimensional NMR investigations of the dynamic conformations of phospholipids and liquid crystals. Office of Scientific and Technical Information (OSTI), May 1996. http://dx.doi.org/10.2172/6429.

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Howell, Steven C. Dynamic Conformations of Nucleosome Arrays in Solution from Small-Angle X-ray Scattering. Office of Scientific and Technical Information (OSTI), January 2016. http://dx.doi.org/10.2172/1338475.

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Markelz, Andrea G. Terahertz Time Domain Spectroscopy of Conformational Dynamics of Sensor Proteins: Basic Research and Pathogen Sensor Development. Fort Belvoir, VA: Defense Technical Information Center, August 2004. http://dx.doi.org/10.21236/ada426482.

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