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Journal articles on the topic 'Structural binding characterization'

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Author: Grafiati

Published: 10 December 2022

Last updated: 28 January 2023

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1

Joseph, Prem Raj B., Ziyan Yuan, Eric A. Kumar, G. L. Lokesh, Smitha Kizhake, Krishna Rajarathnam, and Amarnath Natarajan. "Structural characterization of BRCT–tetrapeptide binding interactions." Biochemical and Biophysical Research Communications 393, no. 2 (March 2010): 207–10. http://dx.doi.org/10.1016/j.bbrc.2010.01.098.

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2

BRIX, Lulu A., Ronald G. DUGGLEBY, Andrea GAEDIGK, and Michael E. McMANUS. "Structural characterization of human aryl sulphotransferases." Biochemical Journal 337, no. 2 (January 8, 1999): 337–43. http://dx.doi.org/10.1042/bj3370337.

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Human aryl sulphotransferase (HAST) 1, HAST3, HAST4 and HAST4v share greater than 90% sequence identity, but vary markedly in their ability to catalyse the sulphonation of dopamine and p-nitrophenol. In order to investigate the amino acid(s) involved in determining differing substrate specificities of HASTs, a range of chimaeric HAST proteins were constructed. Analysis of chimaeric substrate specificities showed that enzyme affinities are mainly determined within the N-terminal end of each HAST protein, which includes two regions of high sequence divergence, termed Regions A (amino acids 44–107) and B (amino acids 132–164). To investigate the substrate-binding sites of HASTs further, site-directed mutagenesis was performed on HAST1 to change 13 individual residues within these two regions to the HAST3 equivalent. A single amino acid change in HAST1 (A146E) was able to change the specificity for p-nitrophenol to that of HAST3. The substrate specificity of HAST1 towards dopamine could not be converted into that of HAST3 with a single amino acid change. However, compared with wild-type HAST1, a number of the mutations resulted in interference with substrate binding, as shown by elevated Ki values towards the co-substrate 3´-phosphoadenosine 5´-phosphosulphate, and in some cases loss of activity towards dopamine. These findings suggest that a co-ordinated change of multiple amino acids in HAST proteins is needed to alter the substrate specificities of these enzymes towards dopamine, whereas a single amino acid at position 146 determines p-nitrophenol affinity. A HAST1 mutant was constructed to express a protein with four amino acids deleted (P87–P90). These amino acids were hypothesized to correspond to a loop region in close proximity to the substrate-binding pocket. Interestingly, the protein showed substrate specificities more similar to wild-type HAST3 than HAST1 and indicates an important role of these amino acids in substrate binding.

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3

Miller, Maria. "Structural Characterization of Transcription Factor C/EBPbeta." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1510. http://dx.doi.org/10.1107/s2053273314084897.

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The basic region:leucine zipper (bZIP) DNA-binding protein, C/EBPbeta, plays a central role in many vital cellular processes, but is also implicated in tumorigenesis, tumor progression, as well as viral replication within cells. C/EBPbeta binds to specific DNA sites as homo- or hetero-dimers and interacts with other transcription factors to control the transcription of a number of eukaryotic genes. C/EBPbeta is an intrinsically repressed protein that is activated in response to growth factors. This study employs a variety of techniques such as sequence analysis, molecular modeling, X-ray crystallography, and mutagenesis to provide structural insights into the mechanisms that modulate the biological activities of C/EBPbeta. Analysis of the primary structure indicates that C/EBPbeta is a largely disordered protein that consists of unstructured regions that have the potential to fold upon binding to molecular partners as well as regions that retain irregular conformations regardless of their environment. Here, a model of the auto-inhibited form of C/EBPbeta is presented as well as the structural basis of its specific dimerization, DNA-binding, and interactions with the p300 transcriptional co-activator.

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4

Culurgioni, Simone, Minzhe Tang, and Martin Austin Walsh. "Structural characterization of theStreptococcus pneumoniaecarbohydrate substrate-binding protein SP0092." Acta Crystallographica Section F Structural Biology Communications 73, no. 1 (January 1, 2017): 54–61. http://dx.doi.org/10.1107/s2053230x16020252.

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Streptococcus pneumoniaeis an opportunistic respiratory pathogen that remains a major cause of morbidity and mortality globally, with infants and the elderly at the highest risk.S. pneumoniaerelies entirely on carbohydrates as a source of carbon and dedicates a third of all uptake systems to carbohydrate import. The structure of the carbohydrate-free substrate-binding protein SP0092 at 1.61 Å resolution reveals it to belong to the newly proposed subclass G of substrate-binding proteins, with a ligand-binding pocket that is large enough to accommodate complex oligosaccharides. SP0092 is a dimer in solution and the crystal structure reveals a domain-swapped dimer with the monomer subunits in a closed conformation but in the absence of carbohydrate ligand. This closed conformation may be induced by dimer formation and could be used as a mechanism to regulate carbohydrate uptake.

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5

Suda, Yasuo, Dalila Marques, John C. Kermode, Shoichi Kusumoto, and Michael Sobel. "Structural characterization of heparin's binding domain for human platelets." Thrombosis Research 69, no. 6 (March 1993): 501–8. http://dx.doi.org/10.1016/0049-3848(93)90054-r.

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6

Bassenden, Angelia, Dmitry Rodionov, Nilu Sabet-Kassouf, Tahereh Haji, Kun Shi, and Albert Berghuis. ""Structural characterization of aminoglycoside modifying enzyme ANT(2"")-Ia"." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C702. http://dx.doi.org/10.1107/s2053273314092973.

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Aminoglycosides are a class of broad-spectrum antibiotics used in the treatment of serious Gram-negative bacterial infections, they target the 16S RNA subunit and upon binding cause errors in translation, eventually inducing a bactericidal effect [1]. Aminoglycoside nucleotidyltransferase (2")-Ia (ANT(2")-Ia) is an aminoglycoside modifying enzyme that prevents aminoglycosides from binding to the ribosomal subunit, making this enzyme a principle candidate structure-based drug design [2]. Characterization of ANT(2")-Ia has been proven to be difficult due to the low stability and solubility of overexpressed protein, where 95% of the protein being expressed is in the form of inclusion bodies [3]. We describe a protocol that has lead to successful expression and purification of ANT(2")-Ia. A successful enzymatic assay has also been adapted and the protein is active and stable under these conditions with a specific activity of 0.14 U/mg. Furthermore, nuclear magnetic resonance (NMR) studies have allowed for the assignment of 144 of the 176 non-proline backbone residues. Substrate binding NMR experiments have shown unique global chemical shift perturbations upon binding ATP and tobramycin, suggesting unique binding sites for each substrate. Structural determination of ANT(2")-Ia using NMR in conjunction with x-ray crystallography can be utilized in order to develop small molecules that will act as more effective aminoglycosides in order to inhibit ANT(2")-Ia from binding and modifying these antibiotics.

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7

Lee, Meng-Hwan, Wen-Lin Lai, Shuen-Fuh Lin, Cheng-Sheng Hsu, Shwu-Huey Liaw, and Ying-Chieh Tsai. "Structural Characterization of Glucooligosaccharide Oxidase from Acremonium strictum." Applied and Environmental Microbiology 71, no. 12 (December 2005): 8881–87. http://dx.doi.org/10.1128/aem.71.12.8881-8887.2005.

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ABSTRACT Glucooligosaccharide oxidase from Acremonium strictum was screened for potential applications in oligosaccharide acid production and carbohydrate detection. This protein is a unique covalent flavoenzyme which catalyzes the oxidation of a variety of carbohydrates with high selectivity for cello- and maltooligosaccharides. Kinetic measurements suggested that this enzyme possesses an open carbohydrate-binding groove, which is mainly composed of two glucosyl-binding subsites. The encoding gene was subsequently cloned, and one intron was detected in the genomic DNA. Large amounts of active enzymes were expressed in Pichia pastoris, with a yield of 300 mg per liter medium. The protein was predicted to share structural homology with plant cytokinin dehydrogenase and related flavoproteins that share a conserved flavin adenine dinucleotide (FAD)-binding domain. The closest sequence matches are those of plant berberine bridge enzyme-like proteins, particularly the characteristic flavinylation site. Unexpectedly, mutation of the putative FAD-attaching residue, H70, to alanine, serine, cysteine, and tyrosine did not abolish the covalent FAD linkage and had little effect on the Km . Instead, the variants displayed k cat values that were 50- to 600-fold lower, indicating that H70 is crucial for efficient redox catalysis, perhaps through modulation of the oxidative power of the flavin.

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8

Su, Hua-Poo, Keith Rickert, Christine Burlein, Kartik Narayan, Marina Bukhtiyarova, Danielle M. Hurzy, Craig A. Stump, et al. "Structural characterization of nonactive site, TrkA-selective kinase inhibitors." Proceedings of the National Academy of Sciences 114, no. 3 (December 30, 2016): E297—E306. http://dx.doi.org/10.1073/pnas.1611577114.

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Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residues from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of—but adjacent to—the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.

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Gangi Setty, Thanuja, Christine Cho, Sowmya Govindappa, Michael A. Apicella, and S. Ramaswamy. "Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site." Acta Crystallographica Section D Biological Crystallography 70, no. 7 (June 24, 2014): 1801–11. http://dx.doi.org/10.1107/s139900471400830x.

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Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteriaFusobacterium nucleatum,Pasteurella multocidaandVibrio choleraeand their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of theHaemophilus influenzaeprotein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.

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10

Ludzia, Patryk, Edward D. Lowe, Gabriele Marcianò, Shabaz Mohammed, Christina Redfield, and Bungo Akiyoshi. "Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein." Structure 29, no. 9 (September 2021): 1014–28. http://dx.doi.org/10.1016/j.str.2021.04.004.

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11

Klein, Brianna J., Khan L. Cox, Suk Min Jang, Rohit K. Singh, Jacques Côté, Michael G. Poirier, and Tatiana G. Kutateladze. "Structural and biophysical characterization of the nucleosome-binding PZP domain." STAR Protocols 2, no. 2 (June 2021): 100479. http://dx.doi.org/10.1016/j.xpro.2021.100479.

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12

Zajonc, Dirk M., Gary D. Ainge, Gavin F. Painter, Wayne B. Severn, and Ian A. Wilson. "Structural Characterization of Mycobacterial Phosphatidylinositol Mannoside Binding to Mouse CD1d." Journal of Immunology 177, no. 7 (September 18, 2006): 4577–83. http://dx.doi.org/10.4049/jimmunol.177.7.4577.

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13

Freire, Filipe, Maria João Romão, Anjos L. Macedo, Susana S. Aveiro, Brian J. Goodfellow, and Ana Luísa Carvalho. "Preliminary structural characterization of human SOUL, a haem-binding protein." Acta Crystallographica Section F Structural Biology and Crystallization Communications 65, no. 7 (June 27, 2009): 723–26. http://dx.doi.org/10.1107/s174430910902291x.

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14

Soragni, Alice, Barbara Zambelli, Marco D. Mukrasch, Jacek Biernat, Sadasivam Jeganathan, Christian Griesinger, Stefano Ciurli, Eckhard Mandelkow, and Markus Zweckstetter. "Structural Characterization of Binding of Cu(II) to Tau Protein†." Biochemistry 47, no. 41 (October 14, 2008): 10841–51. http://dx.doi.org/10.1021/bi8008856.

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15

Noguera, Martín E., Ernesto A. Roman, Juan B. Rigal, Alexandra Cousido-Siah, André Mitschler, Alberto Podjarny, and Javier Santos. "Structural characterization of metal binding to a cold-adapted frataxin." JBIC Journal of Biological Inorganic Chemistry 20, no. 4 (April 2, 2015): 653–64. http://dx.doi.org/10.1007/s00775-015-1251-9.

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16

Beck-Sickinger, Annette G. "Structural characterization and binding sites of G-protein-coupled receptors." Drug Discovery Today 1, no. 12 (December 1996): 502–13. http://dx.doi.org/10.1016/s1359-6446(96)10042-8.

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17

Peana, Massimiliano, Serenella Medici, Valeria Marina Nurchi, Guido Crisponi, and Maria Antonietta Zoroddu. "Nickel binding sites in histone proteins: Spectroscopic and structural characterization." Coordination Chemistry Reviews 257, no. 19-20 (October 2013): 2737–51. http://dx.doi.org/10.1016/j.ccr.2013.02.022.

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18

Castro-Rodrigues, Artur F., Fátima Fonseca, Carol A. Harley, and João H. Morais-Cabral. "Eag K+ Channel Binding to CaMKII: Structural and Biochemical Characterization." Biophysical Journal 108, no. 2 (January 2015): 277a. http://dx.doi.org/10.1016/j.bpj.2014.11.1517.

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19

daCosta, Corrie J. B., R. Michel Sturgeon, Ayman K. Hamouda, Michael P. Blanton, and John E. Baenziger. "Structural characterization and agonist binding to human α4β2 nicotinic receptors." Biochemical and Biophysical Research Communications 407, no. 3 (April 2011): 456–60. http://dx.doi.org/10.1016/j.bbrc.2011.03.026.

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20

Fillaut, Jean-Luc, Isaac de los Rios, Dante Masi, Antonio Romerosa, Fabrizio Zanobini, and Maurizio Peruzzini. "Synthesis and Structural Characterization of (Carbene)ruthenium Complexes Binding Nucleobases." European Journal of Inorganic Chemistry 2002, no. 4 (March 2002): 935–42. http://dx.doi.org/10.1002/1099-0682(200203)2002:4<935::aid-ejic935>3.0.co;2-i.

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21

Briand, Loïc, Claude Nespoulous, Valérie Perez, Jean-Jacques Rémy, Jean-Claude Huet, and Jean-Claude Pernollet. "Ligand-binding properties and structural characterization of a novel rat odorant-binding protein variant." European Journal of Biochemistry 267, no. 10 (May 2000): 3079–89. http://dx.doi.org/10.1046/j.1432-1033.2000.01340.x.

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22

Tang, Heng, Özlem Demir, Fredy Kurniawan, William L. Brown, Ke Shi, Nicholas H. Moeller, Michael A. Carpenter, et al. "Structural Characterization of a Minimal Antibody against Human APOBEC3B." Viruses 13, no. 4 (April 12, 2021): 663. http://dx.doi.org/10.3390/v13040663.

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APOBEC3B (A3B) is one of seven human APOBEC3 DNA cytosine deaminases that restrict viral infections as part of the overall innate immune response, but it also plays a major role in tumor evolution by mutating genomic DNA. Given the importance of A3B as a restriction factor of viral infections and as a driver of multiple human cancers, selective antibodies against A3B are highly desirable for its specific detection in various research and possibly diagnostic applications. Here, we describe a high-affinity minimal antibody, designated 5G7, obtained via a phage display screening against the C-terminal catalytic domain (ctd) of A3B. 5G7 also binds APOBEC3A that is highly homologous to A3Bctd but does not bind the catalytic domain of APOBEC3G, another Z1-type deaminase domain. The crystal structure of 5G7 shows a canonical arrangement of the heavy and light chain variable domains, with their complementarity-determining region (CDR) loops lining an antigen-binding cleft that accommodates a pair of α-helices. To understand the mechanism of A3Bctd recognition by 5G7, we used the crystal structures of A3Bctd and 5G7 as templates and computationally predicted the A3B-5G7 complex structure. Stable binding poses obtained by the simulation were further tested by site-directed mutagenesis and in vitro binding analyses. These studies mapped the epitope for 5G7 to a portion of C-terminal α6 helix of A3Bctd, with Arg374 playing an essential role. The same region of A3Bctd was used previously as a peptide antigen for generating a rabbit monoclonal antibody (mAb 5210-87-13), suggesting that this region is particularly immunogenic and that these antibodies from very different origins may share similar binding modes. Our studies provide a platform for the development of selective antibodies against A3B and other APOBEC3 family enzymes.

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23

Fuller, S. A., A. Philips, and M. S. Coleman. "Affinity purification and refined structural characterization of terminal deoxynucleotidyltransferase." Biochemical Journal 231, no. 1 (October 1, 1985): 105–13. http://dx.doi.org/10.1042/bj2310105.

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A total of 56 stable murine hybridoma monoclones that produce homogeneous antibodies against human or calf terminal deoxynucleotidyltransferase have been established. All of the antibodies exhibited specific binding to various Mr forms of terminal transferase and eight possessed neutralizing activity. Results are presented that permitted characterization of ten of these antibodies with respect to their immunoglobulin class, their recognition of calf or human terminal-transferase Mr species by immunoblotting techniques and their recognition of distinct antigenic sites. Terminal transferase was purified in a single step by using an immunoaffinity column constructed with a monoclonal antibody exhibiting a high binding affinity for the enzyme. Single monoclonal antibodies were also used to bind selectively to terminal-transferase antigen in tissue slices and individual cells.

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24

Hecht, Oliver, Colin Macdonald, and Geoffrey R. Moore. "Intrinsically disordered proteins: lessons from colicins." Biochemical Society Transactions 40, no. 6 (November 21, 2012): 1534–38. http://dx.doi.org/10.1042/bst20120198.

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Defining structural features of IDPs (intrinsically disordered proteins) and relating these to biological function requires characterization of their dynamical properties. In the present paper, we review what is known about the IDPs of colicins, protein antibiotics that use their IDPs to enter bacterial cells. The structurally characterized colicin IDPs we consider contain linear binding epitopes for proteins within their target cells that the colicin hijacks during entry. We show that these binding epitopes take part in intramolecular interactions in the absence of protein partners, i.e. self-recognition, and consider the structural origins of this and its functional implications. We suggest that self-recognition is common in other IDPs that contain similar types of binding epitopes.

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Schiele, Felix, Joanne van Ryn, Keith Canada, Corey Newsome, Eliud Sepulveda, John Park, Herbert Nar, and Tobias Litzenburger. "A specific antidote for dabigatran: functional and structural characterization." Blood 121, no. 18 (May 2, 2013): 3554–62. http://dx.doi.org/10.1182/blood-2012-11-468207.

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Key Points We present an antidote for dabigatran that effectively reverses its anticoagulative effect in human plasma in vitro and in rats in vivo. The antidote shares structural features with thrombin in the mode of binding but has no activity in coagulation tests.

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Chattopadhyay, Rima, Roxana Iacob, Rinku Majumder, Kenneth B. Tomer, and Barry R. Lentz. "Functional and Structural Characterization of Factor Xa Dimer in Solution." Blood 110, no. 11 (November 16, 2007): 2698. http://dx.doi.org/10.1182/blood.v110.11.2698.2698.

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Abstract Previous studies of blood coagulation factor Xa (bovine) showed that binding of water soluble phosphatidylserine (C6PS) to factor Xa (FXa) leads to Ca2+ dependent inactive (∼1000-fold inactivation) dimer formation. We show now that human factor Xa activity is also regulated by C6PS-induced dimerization in the presence of 5 mM Ca2+ We also report that the FXa dimer is inactive: despite the fact dimerization does not block the active site; in part because it does block a substrate exosite; the dimer interface involves lysine residues that boarder the active site and exosites, and the structure of FXa in the dimer is altered relative to the monomer. We have measured initial rates of prothrombin activation (using synthetic thrombin substrate S-2238) at varying FXa and substrate concentrations to show that the kcat/Km decreased (kcat decreased significantly and Km increased slightly) with an increase in FXa dimer formation. The observed significant decrease in kcat indicates that dimerization affects the alignment of substrate with the active site, perhaps through altering substrate binding or through altering the structure of the active site. Amidolytic activity of monomeric FXa (using synthetic substrate S-2765) decreased in response to C6PS binding, while that of the dimer increased slightly. This indicates that dimerization did not block the active site but may alter its conformation. CD and mass spectrometry showed that both Ca2+ and C6PS binding alter FXa structure and that dimerization further alters structure. Acetylation of exposed lysine residues and analysis of MS patterns obtained under conditions that favor either monomer or dimer FXa revealed that the dimerization buries lysines residues 222 and 224 (chymotrypsin numbering) that boarder the active site and are in putative exocytes. We used MS data, fluorescence energy transfer data for active site labeled FXa, to model the FXa dimer structure based on a FXa monomer model (from Gla-domainless Xa X-ray structure and Gla-EGFn with Ca2+) but the requirement that known membrane binding sites or paired FXa molecules would be located in plane was failed. Our lack of success supports our other measurements suggesting that the structure of FXa in a dimer is very different from that in a monomer. Supported by grant from the NHBL (HL 072827 to BRL).

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Nauroozi, Djawed, Benjamin Wurster, and Rüdiger Faust. "Cross-π-conjugated enediyne with multitopic metal binding sites." RSC Advances 10, no. 63 (2020): 38612–16. http://dx.doi.org/10.1039/d0ra06320g.

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Malik, Radhika, and Ronald E. Viola. "Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions." Acta Crystallographica Section D Biological Crystallography 66, no. 6 (May 15, 2010): 673–84. http://dx.doi.org/10.1107/s0907444910008851.

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The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2 Å resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg2+and NADH. This TDH structure fromPseudomonas putidahas a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH.

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29

Edwards, Thomas A., Jose Trincao, Carlos R. Escalante, Robin P. Wharton, and Aneel K. Aggarwal. "Crystallization and Characterization of Pumilio: A Novel RNA Binding Protein." Journal of Structural Biology 132, no. 3 (December 2000): 251–54. http://dx.doi.org/10.1006/jsbi.2000.4319.

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30

Khunrae, Pongsak, and Matthew K. Higgins. "Structural insights into chondroitin sulfate binding in pregnancy-associated malaria." Biochemical Society Transactions 38, no. 5 (September 24, 2010): 1337–41. http://dx.doi.org/10.1042/bst0381337.

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Malaria during pregnancy is caused when parasite-infected erythrocytes accumulate within the placenta through interactions between the VAR2CSA protein on the infected erythrocyte surface and placental CSPGs (chondroitin sulfate proteoglycans). This interaction is the major target for therapeutics to treat or prevent pregnancy-associated malaria. Here we review the structural characterization of CSPG-binding DBL (Duffy-binding like) domains from VAR2CSA and summarize the growing evidence that the exquisite ligand specificity of VAR2CSA results from the adoption of higher-order architecture in which these domains fold together to form a ligand-binding pocket.

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31

KÖSE, Muhammet, Ozge GUNGÖR, Julide NACAROGLU BALLI, and Hilal KIRPIK. "Structural characterization and DNA binding properties of a new imine compound." Cumhuriyet Science Journal 41, no. 2 (June 25, 2020): 407–12. http://dx.doi.org/10.17776/csj.594938.

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32

Clark, Kimber, Lisa Utschig, Thomas V. O'Halloran, and James E. Penner-Hahn. "Structural Characterization of the Binding Site in the MerR Metalloregulatory Protein." Japanese Journal of Applied Physics 32, S2 (January 1, 1993): 536. http://dx.doi.org/10.7567/jjaps.32s2.536.

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33

Kawaguchi, K., T. Yamaki, T. Aizawa, S. Takiya, M. Demura, and K. Nitta. "Structural characterization of DNA binding domain composed of tandem repeat sequence." Seibutsu Butsuri 43, supplement (2003): S41. http://dx.doi.org/10.2142/biophys.43.s41_4.

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34

Muthu, M., and A. J. Sutherland Smith. "Structural and biochemical characterization of actin binding by dystrophin and utrophin." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (August 23, 2008): C296. http://dx.doi.org/10.1107/s0108767308090545.

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35

Yanover, C., and P. Bradley. "Large-scale characterization of peptide-MHC binding landscapes with structural simulations." Proceedings of the National Academy of Sciences 108, no. 17 (April 8, 2011): 6981–86. http://dx.doi.org/10.1073/pnas.1018165108.

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Toledo, Darwin, Arnau Cordomí, Maria Grazia Proietti, Maurizio Benfatto, Luis J. del Valle, Juan J. Pérez, Pere Garriga, and Francesc Sepulcre. "Structural Characterization of a Zinc High-affinity Binding Site in Rhodopsin." Photochemistry and Photobiology 85, no. 2 (March 2009): 479–84. http://dx.doi.org/10.1111/j.1751-1097.2008.00529.x.

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Choi, K. Y., and H. Zalkin. "Structural characterization and corepressor binding of the Escherichia coli purine repressor." Journal of Bacteriology 174, no. 19 (1992): 6207–14. http://dx.doi.org/10.1128/jb.174.19.6207-6214.1992.

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Di Pietro, Santiago M., Betina Córsico, Massimiliano Perduca, Hugo L. Monaco, and José A. Santomé. "Structural and Biochemical Characterization of Toad Liver Fatty Acid-Binding Protein†,‡." Biochemistry 42, no. 27 (July 2003): 8192–203. http://dx.doi.org/10.1021/bi034213n.

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Marshak, Daniel R., Hayato Umekawa, D. Martin Watterson, and Hiroyoshi Hidaka. "Structural characterization of the calcium binding protein S100 from adipose tissue." Archives of Biochemistry and Biophysics 240, no. 2 (August 1985): 777–80. http://dx.doi.org/10.1016/0003-9861(85)90086-4.

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Wei, Xiaoyong. "Characterization of structural requirement for binding of gigantol and aldose reductase." Frontiers in Bioscience 24, no. 6 (2019): 1024–36. http://dx.doi.org/10.2741/4765.

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Ahmad, Syed S., Joseph M. Scandura, and Peter N. Walsh. "Structural and Functional Characterization of Platelet Receptor-mediated Factor VIII Binding." Journal of Biological Chemistry 275, no. 17 (April 21, 2000): 13071–81. http://dx.doi.org/10.1074/jbc.275.17.13071.

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Voelter, W., R. Wacker, M. Franz, T. Maier, and S. Stoeva. "Complete Structural Characterization of a Chitin-Binding Lectin from Mistletoe Extracts." Journal für praktische Chemie 342, no. 8 (October 2000): 812–18. http://dx.doi.org/10.1002/1521-3897(200010)342:8<812::aid-prac812>3.0.co;2-j.

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Yang, Yifei, Camille Keeler, Ivana Y. Kuo, Elias J. Lolis, Michael E. Hodsdon, and Barbara E. Ehrlich. "Characterization of PC2 Cterm Calcium-Binding Interaction and its Structural Implications." Biophysical Journal 108, no. 2 (January 2015): 215a. http://dx.doi.org/10.1016/j.bpj.2014.11.1186.

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Lian, Fu-Ming, Xiangwei Yang, Wancai Yang, Yong-Liang Jiang, and Chengmin Qian. "Structural characterization of the redefined DNA-binding domain of human XPA." Biochemical and Biophysical Research Communications 514, no. 3 (June 2019): 985–90. http://dx.doi.org/10.1016/j.bbrc.2019.05.050.

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Crabb, John W., Yang Cehen, Steve Goldflam, Richard Intres, Karen A. West, Jeffery D. Hulmes, James T. Kapron, et al. "Structural and functional characterization of recombinant human cellular retinaldehyde-binding protein." Protein Science 7, no. 3 (March 1998): 746–57. http://dx.doi.org/10.1002/pro.5560070324.

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Pérez-Payá, Enrique, Behrouz Forood, Richard A. Houghten, and Sylvie E. Blondelle. "Structural characterization and 5′-mononucleotide binding of polyalanine β-sheet complexes." Journal of Molecular Recognition 9, no. 5-6 (October 1996): 488–93. http://dx.doi.org/10.1002/(sici)1099-1352(199634/12)9:5/6<488::aid-jmr289>3.0.co;2-f.

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Xu, Xiaojin, Xueyong Zhu, Raymond A. Dwek, James Stevens, and Ian A. Wilson. "Structural Characterization of the 1918 Influenza Virus H1N1 Neuraminidase." Journal of Virology 82, no. 21 (August 20, 2008): 10493–501. http://dx.doi.org/10.1128/jvi.00959-08.

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ABSTRACT Influenza virus neuraminidase (NA) plays a crucial role in facilitating the spread of newly synthesized virus in the host and is an important target for controlling disease progression. The NA crystal structure from the 1918 “Spanish flu” (A/Brevig Mission/1/18 H1N1) and that of its complex with zanamivir (Relenza) at 1.65-Å and 1.45-Å resolutions, respectively, corroborated the successful expression of correctly folded NA tetramers in a baculovirus expression system. An additional cavity adjacent to the substrate-binding site is observed in N1, compared to N2 and N9 NAs, including H5N1. This cavity arises from an open conformation of the 150 loop (Gly147 to Asp151) and appears to be conserved among group 1 NAs (N1, N4, N5, and N8). It closes upon zanamivir binding. Three calcium sites were identified, including a novel site that may be conserved in N1 and N4. Thus, these high-resolution structures, combined with our recombinant expression system, provide new opportunities to augment the limited arsenal of therapeutics against influenza.

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Harrington, Amanda T., Patricia D. Hearn, Wendy L. Picking, Jeffrey R. Barker, Andrew Wessel, and William D. Picking. "Structural Characterization of the N Terminus of IpaC from Shigella flexneri." Infection and Immunity 71, no. 3 (March 2003): 1255–64. http://dx.doi.org/10.1128/iai.71.3.1255-1264.2003.

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ABSTRACT The primary effector for Shigella invasion of epithelial cells is IpaC, which is secreted via a type III secretion system. We recently reported that the IpaC N terminus is required for type III secretion and possibly other functions. In this study, mutagenesis was used to identify an N-terminal secretion signal and to determine the functional importance of the rest of the IpaC N terminus. The 15 N-terminal amino acids target IpaC for secretion by Shigella flexneri, and placing additional amino acids at the N terminus does not interfere with IpaC secretion. Furthermore, amino acid sequences with no relationship to the native IpaC secretion signal can also direct its secretion. Deletions introduced beyond amino acid 20 have no effect on secretion and do not adversely affect IpaC function in vivo until they extend beyond residue 50, at which point invasion function is completely eliminated. Deletions introduced at amino acid 100 and extending toward the N terminus reduce IpaC's invasion function but do not eliminate it until they extend to the N-terminal side of residue 80, indicating that a region from amino acid 50 to 80 is critical for IpaC invasion function. To explore this further, the ability of an IpaC N-terminal peptide to associate in vitro with its translocon partner IpaB and its chaperone IpgC was studied. The N-terminal peptide binds tightly to IpaB, but the IpaC central hydrophobic region also appears to participate in this binding. The N-terminal peptide also associates with the chaperone IpgC and IpaB is competitive for this interaction. Based on additional biophysical data, we propose that a region between amino acids 50 and 80 is required for chaperone binding, and that the IpaB binding domain is located downstream from, and possibly overlapping, this region. From these data, we propose that the secretion signal, chaperone binding region, and IpaB binding domain are located at the IpaC N terminus and are essential for presentation of IpaC to host cells during bacterial entry; however, IpaC effector activity may be located elsewhere.

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Toku, Seikichi, Isaac K. E. Quaye, and Tatsuo Tanaka. "Isolation and characterization of chicken GA-binding protein." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1579, no. 1 (November 2002): 50–54. http://dx.doi.org/10.1016/s0167-4781(02)00503-1.

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Basore, Katherine, James T. Earnest, Michael S. Diamond, and Daved H. Fremont. "Structural characterization of broadly neutralizing alphavirus antibodies." Journal of Immunology 200, no. 1_Supplement (May 1, 2018): 126.33. http://dx.doi.org/10.4049/jimmunol.200.supp.126.33.

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Abstract Mayaro is a mosquito-borne single-stranded positive RNA alphavirus endemic to tropical regions of South America. It is closely related to other arthritogenic alphaviruses, such as Chikungunya, Semliki Forest, Ross River, and Sindbis viruses. Although there are currently no available vaccines or therapies for alphaviruses, previous studies demonstrate that cross-protection between different alphaviruses could be mediated by antibodies that map to conserved epitopes. For example, a class of monoclonal antibodies against Chikungunya were recently shown to neutralize other alphaviruses by blocking viral entry and egress, all with epitopes on the surface E2 glycoprotein. A panel of antibodies generated against Mayaro infection and boosted with recombinate E2 protein were also found to be cross-neutralizing against other alphaviruses. Currently, epitope mapping and structural studies are being performed on these antibodies in order to determine the vital residues for binding, as well as to determine the mechanism of cross-neutralization.

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