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Journal articles on the topic 'Structural interaction'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

JOHNSTON, RICHARD D., and GEOFFREY W. BARTON. "Structural interaction analysis." International Journal of Control 41, no. 4 (1985): 1005–13. http://dx.doi.org/10.1080/0020718508961179.

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2

Pooler, James. "Structural Spatial Interaction∗." Professional Geographer 45, no. 3 (1993): 297–305. http://dx.doi.org/10.1111/j.0033-0124.1993.00297.x.

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3

Gursoy, Attila, Ozlem Keskin, and Ruth Nussinov. "Topological properties of protein interaction networks from a structural perspective." Biochemical Society Transactions 36, no. 6 (2008): 1398–403. http://dx.doi.org/10.1042/bst0361398.

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Protein–protein interactions are usually shown as interaction networks (graphs), where the proteins are represented as nodes and the connections between the interacting proteins are shown as edges. The graph abstraction of protein interactions is crucial for understanding the global behaviour of the network. In this mini review, we summarize basic graph topological properties, such as node degree and betweenness, and their relation to essentiality and modularity of protein interactions. The classification of hub proteins into date and party hubs with distinct properties has significant implica

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4

ZHU, ZHENGWEI, ANDREY TOVCHIGRECHKO, TATIANA BARONOVA, et al. "LARGE-SCALE STRUCTURAL MODELING OF PROTEIN COMPLEXES AT LOW RESOLUTION." Journal of Bioinformatics and Computational Biology 06, no. 04 (2008): 789–810. http://dx.doi.org/10.1142/s0219720008003679.

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Structural aspects of protein–protein interactions provided by large-scale, genome-wide studies are essential for the description of life processes at the molecular level. A methodology is developed that applies the protein docking approach (GRAMM), based on the knowledge of experimentally determined protein–protein structures (DOCKGROUND resource) and properties of intermolecular energy landscapes, to genome-wide systems of protein interactions. The full sequence-to-structure-of-complex modeling pipeline is implemented in the Genome Wide Docking Database (GWIDD) resource. Protein interaction

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5

Hakes, Luke, David L. Robertson, Stephen G. Oliver, and Simon C. Lovell. "Protein Interactions from Complexes: A Structural Perspective." Comparative and Functional Genomics 2007 (2007): 1–5. http://dx.doi.org/10.1155/2007/49356.

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By combining crystallographic information with protein-interaction data obtained through traditional experimental means, this paper determines the most appropriate method for generating protein-interaction networks that incorporate data derived from protein complexes. We propose that a combined method should be considered; in which complexes composed of five chains or less are decomposed using the matrix model, whereas the spoke model is used to derive pairwise interactions for those with six chains or more. The results presented here should improve the accuracy and relevance of studies invest

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6

Oke, S. A., and M. K. O. Ayomoh. "The hybrid structural interaction matrix." International Journal of Quality & Reliability Management 22, no. 6 (2005): 607–25. http://dx.doi.org/10.1108/02656710510604917.

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7

Guven-Maiorov, Emine, Chung-Jung Tsai, and Ruth Nussinov. "Structural host-microbiota interaction networks." PLOS Computational Biology 13, no. 10 (2017): e1005579. http://dx.doi.org/10.1371/journal.pcbi.1005579.

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8

Anton, M., and F. Casciati. "Structural control against failure interaction." Journal of Structural Control 5, no. 1 (1998): 63–73. http://dx.doi.org/10.1002/stc.4300050104.

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9

Drobakha, Hr, I. Neklonskyi, A. Kateshchenok, et al. "Structural and functional simulation of interaction in the field of aviation safety by using matrices." Archives of Materials Science and Engineering 2, no. 95 (2019): 74–84. http://dx.doi.org/10.5604/01.3001.0013.1734.

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Purpose: The conducted research was aimed at constructing a structural and functional model for the interaction of bodies providing aviation safety during crisis management. Design/methodology/approach: The methods of mathematical simulation and the graph theory, the methods comparison and formalization have been applied to study the process of interaction between the bodies assuring aviation safety. Using methods of the linear algebra allowed constructing a mathematical model for the functional structure of the interaction process that contains description of this process by the main methods

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10

DeBlasio, Stacy L., Juan D. Chavez, Mariko M. Alexander, et al. "Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology." Journal of Virology 90, no. 4 (2015): 1973–87. http://dx.doi.org/10.1128/jvi.01706-15.

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ABSTRACTDemonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus[PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topologica

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11

Kulharia, Mahesh. "Geometrical and electro-static determinants of protein-protein interactions." Bioinformation 17, no. 10 (2021): 851–60. http://dx.doi.org/10.6026/97320630017851.

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Protein-protein interactions (PPI) are pivotal to the numerous processes in the cell. Therefore, it is of interest to document the analysis of these interactions in terms of binding sites, topology of the interacting structures and physiochemical properties of interacting interfaces and the of forces interactions. The interaction interface of obligatory protein-protein complexes differs from that of the transient interactions. We have created a large database of protein-protein interactions containing over100 thousand interfaces. The structural redundancy was eliminated to obtain a non-redunda

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12

Zhang, Heng, Ke Liu, Natsuko Izumi, et al. "Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2." Proceedings of the National Academy of Sciences 114, no. 47 (2017): 12483–88. http://dx.doi.org/10.1073/pnas.1711486114.

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The P-element–induced wimpy testis (PIWI)-interacting RNA (piRNA) pathway plays a central role in transposon silencing and genome protection in the animal germline. A family of Tudor domain proteins regulates the piRNA pathway through direct Tudor domain–PIWI interactions. Tudor domains are known to fulfill this function by binding to methylated PIWI proteins in an arginine methylation-dependent manner. Here, we report a mechanism of methylation-independent Tudor domain–PIWI interaction. Unlike most other Tudor domains, the extended Tudor domain of mammalian Tudor domain-containing protein 2 (

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13

Han, Ying, Liang Cheng, and Weiju Sun. "Analysis of Protein-Protein Interaction Networks through Computational Approaches." Protein & Peptide Letters 27, no. 4 (2020): 265–78. http://dx.doi.org/10.2174/0929866526666191105142034.

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The interactions among proteins and genes are extremely important for cellular functions. Molecular interactions at protein or gene levels can be used to construct interaction networks in which the interacting species are categorized based on direct interactions or functional similarities. Compared with the limited experimental techniques, various computational tools make it possible to analyze, filter, and combine the interaction data to get comprehensive information about the biological pathways. By the efficient way of integrating experimental findings in discovering PPIs and computational

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14

Kholmurotov, Botirzhon, and Muattar Tokhirjonova. "INTERACTION OF RAW COTTON WITH INTERNAL STRUCTURAL ELEMENTS OF DRUM DRYERS." American Journal of Applied sciences 05, no. 06 (2023): 23–28. http://dx.doi.org/10.37547/tajas/volume05issue06-06.

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This research focuses on the study of the interaction between raw cotton and the internal structural elements of drum dryers. A system of equations is presented to analyze the equilibrium of raw cotton clouds on the surface of the blades and the annular layer, determining the conditions for clod sliding or rolling. The conditions necessary for the formation of an annular layer of raw cotton inside the dryer are established. The mechanism of twisting of fibrous bonds during the rolling of excess raw cotton along the annular stand inside the dryer is examined. Examples of the calculation of fibr

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15

Nakashima, Masaaki, Hirotaka Ode, Takashi Kawamura, et al. "Structural Insights into HIV-1 Vif-APOBEC3F Interaction." Journal of Virology 90, no. 2 (2015): 1034–47. http://dx.doi.org/10.1128/jvi.02369-15.

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ABSTRACTThe HIV-1 Vif protein inactivates the cellular antiviral cytidine deaminase APOBEC3F (A3F) in virus-infected cells by specifically targeting it for proteasomal degradation. Several studies identified Vif sequence motifs involved in A3F interaction, whereas a Vif-binding A3F interface was proposed based on our analysis of highly similar APOBEC3C (A3C). However, the structural mechanism of specific Vif-A3F recognition is still poorly understood. Here we report structural features of interaction interfaces for both HIV-1 Vif and A3F molecules. Alanine-scanning analysis of Vif revealed tha

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16

Hu, Zhengyu, and Yuzhu Li. "NUMERICAL STUDY ON THE INTERACTION BETWEEN PERIODIC WAVES AND A FLEXIBLE WALL." Coastal Engineering Proceedings, no. 37 (September 1, 2023): 3. http://dx.doi.org/10.9753/icce.v37.structures.3.

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Coastal structures were usually considered as stiff in the majority of studies related to wave structure interaction I n certain situations, such as impulsive wave loading on flexible breakwaters, ship hulls, tank walls hydroelasticity can be of importance for both wave dynamics and structural responses Akrish et al. (2018) showed that hydroelastic effects can either relax or amplify the hydrodynamic characteristics (i.e., wave run up and force) and structural oscillations in a deformable cantilever wal l interacting with an incident wave group. For flexible coastal defenses, Huang and Li (202

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17

Roy, Paushali, and Abhijit Datta. "DCL and Associated Proteins of Arabidopsis thaliana - An Interaction Study." International Letters of Natural Sciences 61 (January 2017): 85–94. http://dx.doi.org/10.18052/www.scipress.com/ilns.61.85.

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During RNA interference in plants, Dicer-like/DCL proteins process longer double-stranded RNA (dsRNA) precursors into small RNA molecules. In Arabidopsis thaliana there are four DCLs (DCL1, DCL2, DCL3, and DCL4) that interact with various associated proteins to carry out this processing. The lack of complete structural-functional information and characterization of DCLs and their associated proteins leads to this study where we have generated the structures by modelling, analysed the structures and studied the interactions of Arabidopsisthaliana DCLs with their associated proteins with the hom

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18

Khakzad, Hamed, Lotta Happonen, Yasaman Karami, et al. "Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology." PLOS Computational Biology 17, no. 1 (2021): e1008169. http://dx.doi.org/10.1371/journal.pcbi.1008169.

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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 su

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19

Malenov, Dusan, and Snezana Zaric. "Parallel interactions of aromatic and heteroaromatic molecules." Chemical Industry 70, no. 6 (2016): 649–59. http://dx.doi.org/10.2298/hemind151009003m.

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Parallel interactions of aromatic and heteroaromatic molecules are very important in chemistry and biology. In this review, recent findings on preferred geometries and interaction energies of these molecules are presented. Benzene and pyridine were used as model systems for studying aromatic and heteroaromatic molecules, respectively. Searches of Cambridge Structural Database show that both aromatic and heteroaromatic molecules prefer interacting at large horizontal displacements, even though previous calculations showed that stacking interactions (with offsets of about 1.5 ?) are the stronges

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20

Paik, Youngsuk. "Analysis of the Structural Relationship Among Early Childhood Teachers' Empathy Ability, Teacher-Child Interaction, and Children's Peer Play Interaction." Korean Association For Learner-Centered Curriculum And Instruction 23, no. 22 (2023): 223–38. http://dx.doi.org/10.22251/jlcci.2023.23.22.223.

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Objectives To set the empathic ability of early childhood teachers, which affects young children's peer play interactions, as an independent variable and teacher-child interaction as a mediating variable, and to analyze the structural relationship between the variables. Methods A survey was conducted targeting 91 early childhood teachers and 343 5-year-old children located in S City, G Province, K City, and J Province to confirm the structural relationship between variables related to children's peer play interaction, and the collected data conducted path analysis using structural equati

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21

Chory, M. A., M. D. Roesler, V. A. Spector, E. Bayo, H. Flashner, and F. Jabbari. "Control Structural Interaction Testbed: A Model for University Industry Interaction." IFAC Proceedings Volumes 25, no. 12 (1991): 97–102. http://dx.doi.org/10.1016/s1474-6670(17)50096-8.

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22

Nicoludis, John M., Anna G. Green, Sanket Walujkar, et al. "Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis." Proceedings of the National Academy of Sciences 116, no. 36 (2019): 17825–30. http://dx.doi.org/10.1073/pnas.1821063116.

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Clustered protocadherins, a large family of paralogous proteins that play important roles in neuronal development, provide an important case study of interaction specificity in a large eukaryotic protein family. A mammalian genome has more than 50 clustered protocadherin isoforms, which have remarkable homophilic specificity for interactions between cellular surfaces. A large antiparallel dimer interface formed by the first 4 extracellular cadherin (EC) domains controls this interaction. To understand how specificity is achieved between the numerous paralogs, we used a combination of structura

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23

Djinovic-Carugo, Kristina, and Oliviero Carugo. "Structural Portrait of Filamin Interaction Mechanisms." Current Protein & Peptide Science 11, no. 7 (2010): 639–50. http://dx.doi.org/10.2174/138920310794109111.

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24

Kovačič, Lidija, Nejc Paulič, Adrijana Leonardi, et al. "Structural insight into LexA–RecA* interaction." Nucleic Acids Research 41, no. 21 (2013): 9901–10. http://dx.doi.org/10.1093/nar/gkt744.

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25

Herbst, Sabine, Noa Lipstein, Olaf Jahn, and Andrea Sinz. "Structural insights into calmodulin/Munc13 interaction." Biological Chemistry 395, no. 7-8 (2014): 763–68. http://dx.doi.org/10.1515/hsz-2014-0134.

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Abstract Munc13 proteins are essential presynaptic regulators that mediate synaptic vesicle priming and play a role in the regulation of neuronal short-term synaptic plasticity. All four Munc13 isoforms share a common domain structure, including a calmodulin (CaM) binding site in their otherwise divergent N-termini. Here, we summarize recent results on the investigation of the CaM/Munc13 interaction. By combining chemical cross-linking, photoaffinity labeling, and mass spectrometry, we showed that all neuronal Munc13 isoforms exhibit similar CaM binding modes. Moreover, we demonstrated that th

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26

Chi, Seung-Wook, Si-Hyung Lee, Do-Hyoung Kim, et al. "Structural Details on mdm2-p53 Interaction." Journal of Biological Chemistry 280, no. 46 (2005): 38795–802. http://dx.doi.org/10.1074/jbc.m508578200.

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27

Yousef, Mohammad S., and Brian W. Matthews. "Structural Basis of Prospero-DNA Interaction." Structure 13, no. 4 (2005): 601–7. http://dx.doi.org/10.1016/j.str.2005.01.023.

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28

STALKER, RUTH, and IAN F. C. SMITH. "Structural monitoring using engineer–computer interaction." Artificial Intelligence for Engineering Design, Analysis and Manufacturing 16, no. 3 (2002): 203–18. http://dx.doi.org/10.1017/s0890060402163062.

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Engineer–computer interaction (ECI) is a new subdomain of human–computer interaction that is specifically tailored to engineers' needs. ECI uses an information classification schema, provides a modular approach to task decomposition, and integrates standard engineering characteristics and working procedures into software. A software tool kit that interprets monitoring data taken from bridges was developed according to ECI guidelines. This tool kit was given to engineers for testing and evaluation. An empirical evaluation using questionnaires was performed. The results show that this ECI softwa

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29

Liu, Shitao. "Inverse problem for structural acoustic interaction." Nonlinear Analysis: Theory, Methods & Applications 74, no. 7 (2011): 2647–62. http://dx.doi.org/10.1016/j.na.2010.12.020.

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30

Jackson, Verity A., Daniel del Toro, Maria Carrasquero, et al. "Structural Basis of Latrophilin-FLRT Interaction." Structure 23, no. 4 (2015): 774–81. http://dx.doi.org/10.1016/j.str.2015.01.013.

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31

Duncan, Starkey. "A Structural–Interactionalist Approach to Interaction." Contemporary Psychology: A Journal of Reviews 37, no. 1 (1992): 30–31. http://dx.doi.org/10.1037/031779.

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32

Hadid, Mohamed, and Mounir K. Berrah. "Structural response for stochastic kinematic interaction." Earthquake Engineering & Structural Dynamics 30, no. 1 (2000): 97–114. http://dx.doi.org/10.1002/1096-9845(200101)30:1<97::aid-eqe998>3.0.co;2-t.

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33

Okunevich, E. S., V. Yu Smelov, S. A. Sheremetyeva, V. L. Shper, and E. I. Khunuzidi. "CROSS-STRUCTURAL INTERACTION IN MODERN ORGANIZATIONS." Izvestiya of Samara Scientific Center of the Russian Academy of Sciences 25, no. 1 (2023): 55–66. http://dx.doi.org/10.37313/1990-5378-2023-25-1-55-66.

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The article presents the results of a cross-structural interaction study in modern organizations. The theoretical foundations and reasons for the between-department-barrier emergence are discussed in details. Particular attention is paid to the viewpoint of Dr. E. Deming on the problem of cross-structural interaction, as well as the system-statistical proposals how to eliminate this problem are given.

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34

Hirai, M., T. Takizawa, S. Yabuki, Y. Nakata, S. Arai, and M. Furusaka. "Structural study of protein-ganglioside interaction." Progress in Colloid & Polymer Science 106, no. 1 (1997): 237–41. http://dx.doi.org/10.1007/bf01189528.

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35

Martin, Juliette, Leslie Regad, Hélène Lecornet, and Anne-Claude Camproux. "Structural deformation upon protein-protein interaction: A structural alphabet approach." BMC Structural Biology 8, no. 1 (2008): 12. http://dx.doi.org/10.1186/1472-6807-8-12.

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36

Virtanen, Valtteri, Susanna Räikkönen, Elina Puljula, and Maarit Karonen. "Ellagitannin–Lipid Interaction by HR-MAS NMR Spectroscopy." Molecules 26, no. 2 (2021): 373. http://dx.doi.org/10.3390/molecules26020373.

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Ellagitannins have antimicrobial activity, which might be related to their interactions with membrane lipids. We studied the interactions of 12 different ellagitannins and pentagalloylglucose with a lipid extract of Escherichia coli by high-resolution magic angle spinning NMR spectroscopy. The nuclear Overhauser effect was utilized to measure the cross relaxation rates between ellagitannin and lipid protons. The shifting of lipid signals in 1H NMR spectra of ellagitannin–lipid mixture due to ring current effect was also observed. The ellagitannins that showed interaction with lipids had clear

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37

Moon, F. C., and E. H. Dowell. "Structural Dynamics." Applied Mechanics Reviews 38, no. 10 (1985): 1287–89. http://dx.doi.org/10.1115/1.3143694.

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While much of the linear theory of structural dynamics has been codified in numerous computer software, important problems remain such as inverse methods (modal synthesis or system identification) and optimization problems. Nonlinear problems, however, are a fertile ground for new research, especially those involving large deformations (e.g., crash simulation) and material nonlinearities. Structure interaction problems will continue to be a fruitful area of research including fluid-structure dynamics and interaction with acoustic noise, thermal fields, soils, and electromagnetic forces. For ex

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38

Lee, Bong-Jin. "S2c2-1 Structure and Protein-Protein Interaction of Helicobacter Pylori Proteins(S2-c2: "Structural biology reveals macromolecular interaction",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S127. http://dx.doi.org/10.2142/biophys.46.s127_4.

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39

Hara, Kodai, Masayuki Uchida, Risa Tagata, et al. "Structure of proliferating cell nuclear antigen (PCNA) bound to an APIM peptide reveals the universality of PCNA interaction." Acta Crystallographica Section F Structural Biology Communications 74, no. 4 (2018): 214–21. http://dx.doi.org/10.1107/s2053230x18003242.

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Proliferating cell nuclear antigen (PCNA) provides a molecular platform for numerous protein–protein interactions in DNA metabolism. A large number of proteins associated with PCNA have a well characterized sequence termed the PCNA-interacting protein box motif (PIPM). Another PCNA-interacting sequence termed the AlkB homologue 2 PCNA-interacting motif (APIM), comprising the five consensus residues (K/R)-(F/Y/W)-(L/I/V/A)-(L/I/V/A)-(K/R), has also been identified in various proteins. In contrast to that with PIPM, the PCNA–APIM interaction is less well understood. Here, the crystal structure o

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Roy, Paushali, and Abhijit Datta. "DCL and Associated Proteins of <i>Arabidopsis thaliana </i>- An Interaction Study." International Letters of Natural Sciences 61 (January 10, 2017): 85–94. http://dx.doi.org/10.56431/p-p7a5s1.

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During RNA interference in plants, Dicer-like/DCL proteins process longer double-stranded RNA (dsRNA) precursors into small RNA molecules. In Arabidopsis thaliana there are four DCLs (DCL1, DCL2, DCL3, and DCL4) that interact with various associated proteins to carry out this processing. The lack of complete structural-functional information and characterization of DCLs and their associated proteins leads to this study where we have generated the structures by modelling, analysed the structures and studied the interactions of Arabidopsisthaliana DCLs with their associated proteins with the hom

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41

P., Anitha, G. Swetha R., Anbarasu Anand, and Ramaiah Sudha. "Cation-pi interaction in metalloproteins : A bioinformatics approach." Journal of Indian Chemical Society Vol. 92, Apr 2015 (2015): 518–20. https://doi.org/10.5281/zenodo.5596007.

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Bioinformatics Division, School of BioSciences and Technology, VIT University, Vellore-632 014, Tamilnadu, India <em>E-mail</em> : sudhaanand@vit.ac.in Cation-pi interaction plays an important role in protein structure stability. In our present study, we have analyzed influence of cation-pi interaction in structural stability of metalloproteins. We observed that cation-pi interactions of Arg/Lys-pi interactions might have a significant role in the global conformational stability of metalloproteins. Though Trp residues have lower natural occurrence (1.76%) in proteins but it’s shown the h

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Zhao, Shuang, Yan-Yan Zhu, Xiao-Yu Wang, et al. "Structural Insight into the Interactions between Structurally Similar Inhibitors and SIRT6." International Journal of Molecular Sciences 21, no. 7 (2020): 2601. http://dx.doi.org/10.3390/ijms21072601.

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Sirtuin 6 (SIRT6) is an NAD+-dependent deacetylase with a significant role in 20% of all cancers, such as colon cancers and rectal adenocarcinoma. However, there is currently no effective drug for cancers related to SIRT6. To explore potential inhibitors of SIRT6, it is essential to reveal details of the interaction mechanisms between inhibitors and SIRT6 at the atomic level. The nature of small molecules from herbs have many advantages as inhibitors. Based on the conformational characteristics of the inhibitor Compound 9 (Asinex ID: BAS13555470), we explored the natural molecule Scutellarin,

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43

Vassiliev, Pavel, Evgenii Gusev, Maria Komelkova, Andrey Kochetkov, Maria Dobrynina, and Alexey Sarapultsev. "Computational Analysis of CD46 Protein Interaction with SARS-CoV-2 Structural Proteins: Elucidating a Putative Viral Entry Mechanism into Human Cells." Viruses 15, no. 12 (2023): 2297. http://dx.doi.org/10.3390/v15122297.

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This study examines an unexplored aspect of SARS-CoV-2 entry into host cells, which is widely understood to occur via the viral spike (S) protein’s interaction with human ACE2-associated proteins. While vaccines and inhibitors targeting this mechanism are in use, they may not offer complete protection against reinfection. Hence, we investigate putative receptors and their cofactors. Specifically, we propose CD46, a human membrane cofactor protein, as a potential putative receptor and explore its role in cellular invasion, acting possibly as a cofactor with other viral structural proteins. Empl

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Gautam, Narayan, and Narayan Prasad Adhikari. "Structural characterization of HDAC2-MTA1 complex." BIBECHANA 22, no. 2 (2025): 108–15. https://doi.org/10.3126/bibechana.v22i2.74254.

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Histone deacetylases are recruited to specific transcriptional repression complexes through interactions with corepressor proteins. This recruitment leads to chromatin condensation and transcriptional silencing. In this study, we modeled the complex structure of HDAC2 with MTA1 and investigated the HDAC2 and MTA1 interactions using all-atom molecular dynamics (MD) simulation. Our results show that the ELM2-SANT domains of MTA1 wrap completely around HDAC2. We identified the different types of interactions such as hydrogen bonds, salt bridges, and hydrophobic interactions. Specifically, GLU186,

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45

Larsen, Andreas Haahr. "Understanding cytokinesis interaction by interaction." Structure 32, no. 2 (2024): 120–21. http://dx.doi.org/10.1016/j.str.2024.01.001.

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46

Lim, Jia Jia, Youngjin Lee, Tue Tu Ly, et al. "Structural insights into the interaction of p97 N-terminus domain and VBM in rhomboid protease, RHBDL4." Biochemical Journal 473, no. 18 (2016): 2863–80. http://dx.doi.org/10.1042/bcj20160237.

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RHBDL4 is an active rhomboid that specifically recognizes and cleaves atypical, positively charged transmembrane endoplasmic reticulum-associated degradation (ERAD) substrates. Interaction of valosin-containing protein (p97/VCP) and RHBDL4 is crucial to retrotranslocate polyubiquitinated substrates for ERAD pathway. Here, we report the first complex structure of VCP-binding motif (VBM) with p97 N-terminal domain (p97N) at 1.88 Å resolution. Consistent with p97 adaptor proteins including p47-ubiquitin regulatory X (UBX), gp78-VCP-interacting motif (VIM), OTU1-UBX-like element, and FAF1-UBX, RHB

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Suresh, V., Liang Liu, Donald Adjeroh, and Xiaobo Zhou. "RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information." Nucleic Acids Research 43, no. 3 (2015): 1370–79. http://dx.doi.org/10.1093/nar/gkv020.

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Abstract RNA-protein complexes are essential in mediating important fundamental cellular processes, such as transport and localization. In particular, ncRNA-protein interactions play an important role in post-transcriptional gene regulation like mRNA localization, mRNA stabilization, poly-adenylation, splicing and translation. The experimental methods to solve RNA-protein interaction prediction problem remain expensive and time-consuming. Here, we present the RPI-Pred (RNA-protein interaction predictor), a new support-vector machine-based method, to predict protein-RNA interaction pairs, based

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Stubbs II, Milton T. "Structural Aspects of Factor Xa Inhibition." Current Pharmaceutical Design 2, no. 5 (1996): 543–52. http://dx.doi.org/10.2174/1381612802666221004181847.

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Factor Xa is responsible for both extrinsic and intrinsic generation of active thrombin. The recent structure determination of human factor Xa provides a basis for structure based drug design. Until very recently, however, it .has not been possible to analyse factor Xa - ligand interactions directly. A semi-conservative modelling approach, in which the interaction of factor Xa inhibitors with related serine proteinases is investigated, has yielded valuable information on the structural determinants for factor Xa inhibition. The interactions of factor Xa with DX9065a, tissue factor pathway inhi

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Golubeva, Volha A., Thales C. Nepomuceno, Giuliana de Gregoriis, et al. "Network of Interactions between ZIKA Virus Non-Structural Proteins and Human Host Proteins." Cells 9, no. 1 (2020): 153. http://dx.doi.org/10.3390/cells9010153.

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The Zika virus (ZIKV) is a mosquito-borne Flavivirus and can be transmitted through an infected mosquito bite or through human-to-human interaction by sexual activity, blood transfusion, breastfeeding, or perinatal exposure. After the 2015–2016 outbreak in Brazil, a strong link between ZIKV infection and microcephaly emerged. ZIKV specifically targets human neural progenitor cells, suggesting that proteins encoded by ZIKV bind and inactivate host cell proteins, leading to microcephaly. Here, we present a systematic annotation of interactions between human proteins and the seven non-structural

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Li, Zoe, Ruili Huang, Menghang Xia, Tucker A. Patterson, and Huixiao Hong. "Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery." Biomolecules 14, no. 1 (2024): 72. http://dx.doi.org/10.3390/biom14010072.

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Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein–ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure–activity/property relationship analysis, have gained prominence. Molecular fingerprints encode molecular structures and serve as property profiles, which are essential in drug discovery. While two-dimensional (2D) fingerprints are commonly used, three-dimensional (3D) struc

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