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Journal articles on the topic 'Protein surfaces'

Author: Grafiati

Published: 4 June 2021

Last updated: 15 February 2022

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1

Khan, Mohammad Ashhar I., Ulrich Weininger, Sven Kjellström, Shashank Deep, and Mikael Akke. "Adsorption of unfolded Cu/Zn superoxide dismutase onto hydrophobic surfaces catalyzes its formation of amyloid fibrils." Protein Engineering, Design and Selection 32, no. 2 (2019): 77–85. http://dx.doi.org/10.1093/protein/gzz033.

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Abstract Intracellular aggregates of superoxide dismutase 1 (SOD1) are associated with amyotrophic lateral sclerosis. In vivo, aggregation occurs in a complex and dense molecular environment with chemically heterogeneous surfaces. To investigate how SOD1 fibril formation is affected by surfaces, we used an in vitro model system enabling us to vary the molecular features of both SOD1 and the surfaces, as well as the surface area. We compared fibril formation in hydrophilic and hydrophobic sample wells, as a function of denaturant concentration and extraneous hydrophobic surface area. In the pre

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2

SHRESTHA, NRIPENDRA L., YOUHEI KAWAGUCHI, and TAKENAO OHKAWA. "SUMOMO: A PROTEIN SURFACE MOTIF MINING MODULE." International Journal of Computational Intelligence and Applications 04, no. 04 (2004): 431–49. http://dx.doi.org/10.1142/s1469026804001392.

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Protein surface motifs, which can be defined as commonly appearing patterns of shape and physical properties in protein molecular surfaces, can be considered "possible active sites". We have developed a system for mining surface motifs: SUMOMO which consists of two phases: surface motif extraction and surface motif filtering. In the extraction phase, a given set of protein molecular surface data is divided into small surfaces called unit surfaces. After extracting several common unit surfaces as candidate motifs, they are repetitively merged into surface motifs. However, a large amount of surf

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3

Znamenskiy, Denis, Khan Le Tuan, Anne Poupon, Jacques Chomilier та Jean-Paul Mornon. "β-Sheet modeling by helical surfaces". Protein Engineering, Design and Selection 13, № 6 (2000): 407–12. http://dx.doi.org/10.1093/protein/13.6.407.

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4

Connolly, Michael L. "Plotting protein surfaces." Journal of Molecular Graphics 4, no. 2 (1986): 93–96. http://dx.doi.org/10.1016/0263-7855(86)80004-2.

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5

Kurnik, Martin, Gabriel Ortega, Philippe Dauphin-Ducharme, Hui Li, Amanda Caceres, and Kevin W. Plaxco. "Quantitative measurements of protein−surface interaction thermodynamics." Proceedings of the National Academy of Sciences 115, no. 33 (2018): 8352–57. http://dx.doi.org/10.1073/pnas.1800287115.

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Whereas proteins generally remain stable upon interaction with biological surfaces, they frequently unfold on and adhere to artificial surfaces. Understanding the physicochemical origins of this discrepancy would facilitate development of protein-based sensors and other technologies that require surfaces that do not compromise protein structure and function. To date, however, only a small number of such artificial surfaces have been reported, and the physics of why these surfaces support functional biomolecules while others do not has not been established. Thus motivated, we have developed an

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6

Ban, Yih-En Andrew, Herbert Edelsbrunner, and Johannes Rudolph. "Interface surfaces for protein-protein complexes." Journal of the ACM 53, no. 3 (2006): 361–78. http://dx.doi.org/10.1145/1147954.1147957.

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7

Lehnfeld, J., Y. Dukashin, J. Mark, et al. "Saliva and Serum Protein Adsorption on Chemically Modified Silica Surfaces." Journal of Dental Research 100, no. 10 (2021): 1047–54. http://dx.doi.org/10.1177/00220345211022273.

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Biomaterials, once inserted in the oral cavity, become immediately covered by a layer of adsorbed proteins that consists mostly of salivary proteins but also of plasma proteins if the biomaterial is placed close to the gingival margin or if it becomes implanted into tissue and bone. It is often this protein layer, rather than the pristine biomaterial surface, that is subsequently encountered by colonizing bacteria or attaching tissue cells. Thus, to study this important initial protein adsorption from human saliva and serum and how it might be influenced through chemical modification of the bi

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8

Schricker, Scott R., Manuel L. B. Palacio, and Bharat Bhushan. "Designing nanostructured block copolymer surfaces to control protein adhesion." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 370, no. 1967 (2012): 2348–80. http://dx.doi.org/10.1098/rsta.2011.0484.

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The profile and conformation of proteins that are adsorbed onto a polymeric biomaterial surface have a profound effect on its in vivo performance. Cells and tissue recognize the protein layer rather than directly interact with the surface. The chemistry and morphology of a polymer surface will govern the protein behaviour. So, by controlling the polymer surface, the biocompatibility can be regulated. Nanoscale surface features are known to affect the protein behaviour, and in this overview the nanostructure of self-assembled block copolymers will be harnessed to control protein behaviour. The

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9

Wach, Jean-Yves, Barbora Malisova, Simone Bonazzi, et al. "Protein-Resistant Surfaces through Mild Dopamine Surface Functionalization." Chemistry - A European Journal 14, no. 34 (2008): 10579–84. http://dx.doi.org/10.1002/chem.200801134.

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10

Hato, Masakatsu, Masami Murata, and Takeshi Yoshida. "Surface forces between protein A adsorbed mica surfaces." Colloids and Surfaces A: Physicochemical and Engineering Aspects 109 (April 1996): 345–61. http://dx.doi.org/10.1016/0927-7757(95)03466-8.

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11

Janc, Tadeja, Jean-Pierre Korb, Miha Lukšič, et al. "Multiscale Water Dynamics on Protein Surfaces: Protein-Specific Response to Surface Ions." Journal of Physical Chemistry B 125, no. 31 (2021): 8673–81. http://dx.doi.org/10.1021/acs.jpcb.1c02513.

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12

Mateos, Helena, Alessandra Valentini, Francesco Lopez, and Gerardo Palazzo. "Surfactant Interactions with Protein-Coated Surfaces: Comparison between Colloidal and Macroscopically Flat Surfaces." Biomimetics 5, no. 3 (2020): 31. http://dx.doi.org/10.3390/biomimetics5030031.

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Surface interactions with polymers or proteins are extensively studied in a range of industrial and biomedical applications to control surface modification, cleaning, or biofilm formation. In this study we compare surfactant interactions with protein-coated silica surfaces differing in the degree of curvature (macroscopically flat and colloidal nanometric spheres). The interaction with a flat surface was probed by means of surface plasmon resonance (SPR) while dynamic light scattering (DLS) was used to study the interaction with colloidal SiO2 (radius 15 nm). First, the adsorption of bovine se

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13

Rooklin, David, Ashley E. Modell, Haotian Li, Viktoriya Berdan, Paramjit S. Arora, and Yingkai Zhang. "Targeting Unoccupied Surfaces on Protein–Protein Interfaces." Journal of the American Chemical Society 139, no. 44 (2017): 15560–63. http://dx.doi.org/10.1021/jacs.7b05960.

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14

CAMARERO, JULIO A. "NEW DEVELOPMENTS FOR THE SITE-SPECIFIC ATTACHMENT OF PROTEIN TO SURFACES." Biophysical Reviews and Letters 01, no. 01 (2006): 1–28. http://dx.doi.org/10.1142/s1793048006000045.

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Protein immobilization on surfaces is of great importance in numerous applications in biology and biophysics. The key for the success of all these applications relies on the immobilization technique employed to attach the protein to the corresponding surface. Protein immobilization can be based on covalent or noncovalent interaction of the molecule with the surface. Noncovalent interactions include hydrophobic interactions, hydrogen bonding, van der Waals forces, electrostatic forces, or physical adsorption. However, since these interactions are weak, the molecules can get denatured or dislodg

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15

Messina, G. M. L., C. Bonaccorso, A. Rapisarda, B. Castroflorio, D. Sciotto, and G. Marletta. "Biomimetic protein-harpooning surfaces." MRS Communications 8, no. 02 (2018): 241–47. http://dx.doi.org/10.1557/mrc.2018.54.

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16

Wörz, A., B. Berchtold, K. Moosmann, O. Prucker, and J. Rühe. "Protein-resistant polymer surfaces." Journal of Materials Chemistry 22, no. 37 (2012): 19547. http://dx.doi.org/10.1039/c2jm30820g.

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17

Barberi, Jacopo, and Silvia Spriano. "Titanium and Protein Adsorption: An Overview of Mechanisms and Effects of Surface Features." Materials 14, no. 7 (2021): 1590. http://dx.doi.org/10.3390/ma14071590.

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Titanium and its alloys, specially Ti6Al4V, are among the most employed materials in orthopedic and dental implants. Cells response and osseointegration of implant devices are strongly dependent on the body–biomaterial interface zone. This interface is mainly defined by proteins: They adsorb immediately after implantation from blood and biological fluids, forming a layer on implant surfaces. Therefore, it is of utmost importance to understand which features of biomaterials surfaces influence formation of the protein layer and how to guide it. In this paper, relevant literature of the last 15 y

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18

Bommineni, Praveen K., and Sudeep N. Punnathanam. "Enhancement of nucleation of protein crystals on nano-wrinkled surfaces." Faraday Discussions 186 (2016): 187–97. http://dx.doi.org/10.1039/c5fd00119f.

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The synthesis of high quality protein crystals is essential for determining their structure. Hence the development of strategies to facilitate the nucleation of protein crystals is of prime importance. Recently, Ghatak and Ghatak [Langmuir 2013, 29, 4373] reported heterogeneous nucleation of protein crystals on nano-wrinkled surfaces. Through a series of experiments on different proteins, they were able to obtain high quality protein crystals even at low protein concentrations and sometimes without the addition of a precipitant. In this study, the mechanism of protein crystal nucleation on nan

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19

Alsop, E., M. Silver, and D. R. Livesay. "Optimized electrostatic surfaces parallel increased thermostability: a structural bioinformatic analysis." Protein Engineering Design and Selection 16, no. 12 (2003): 871–74. http://dx.doi.org/10.1093/protein/gzg131.

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20

Via, A., F. Ferrè, B. Brannetti, and M. Helmer-Citterich*. "Protein surface similarities: a survey of methods to describe and compare protein surfaces." Cellular and Molecular Life Sciences 57, no. 13 (2000): 1970–77. http://dx.doi.org/10.1007/pl00000677.

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21

Kim, Jonghwa, Yizhi Tao, Karin M. Reinisch, Stephen C. Harrison, and Max L. Nibert. "Orthoreovirus and Aquareovirus core proteins: conserved enzymatic surfaces, but not protein–protein interfaces." Virus Research 101, no. 1 (2004): 15–28. http://dx.doi.org/10.1016/j.virusres.2003.12.003.

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22

Mehio, Wissam, Graham J. L. Kemp, Paul Taylor, and Malcolm D. Walkinshaw. "Identification of protein binding surfaces using surface triplet propensities." Bioinformatics 26, no. 20 (2010): 2549–55. http://dx.doi.org/10.1093/bioinformatics/btq490.

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23

Eyrisch, Susanne, and Volkhard Helms. "Transient Pockets on Protein Surfaces Involved in Protein−Protein Interaction." Journal of Medicinal Chemistry 50, no. 15 (2007): 3457–64. http://dx.doi.org/10.1021/jm070095g.

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24

Bayer, Peter, Anja Matena, and Christine Beuck. "NMR Spectroscopy of supramolecular chemistry on protein surfaces." Beilstein Journal of Organic Chemistry 16 (October 9, 2020): 2505–22. http://dx.doi.org/10.3762/bjoc.16.203.

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As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein–protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.

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25

Sael, Lee, and Daisuke Kihara. "Characterization and Classification of Local Protein Surfaces Using Self-Organizing Map." International Journal of Knowledge Discovery in Bioinformatics 1, no. 1 (2010): 32–47. http://dx.doi.org/10.4018/jkdb.2010100203.

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Annotating protein structures is an urgent task as increasing number of protein structures of unknown function is being solved. To achieve this goal, it is critical to establish computational methods for characterizing and classifying protein local structures. The authors analyzed the similarity of local surface patches from 609 representative proteins considering shape and the electrostatic potential, which are represented by the 3D Zernike descriptors. Classification of local patches is done with the emergent self-organizing map (ESOM). They mapped patches at ligand binding-sites to investig

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26

Messina, G. M. L., C. Bonaccorso, A. Rapisarda, B. Castroflorio, D. Sciotto, and G. Marletta. "Biomimetic protein-harpooning surfaces – CORRIGENDUM." MRS Communications 8, no. 02 (2018): 624. http://dx.doi.org/10.1557/mrc.2018.116.

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27

Smith, James P., and Vicki Hinson-Smith. "Mapping protein surfaces by MS." Analytical Chemistry 77, no. 19 (2005): 373 A. http://dx.doi.org/10.1021/ac053484w.

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28

Hlady, Vladimir, and Jos Buijs. "Protein adsorption on solid surfaces." Current Opinion in Biotechnology 7, no. 1 (1996): 72–77. http://dx.doi.org/10.1016/s0958-1669(96)80098-x.

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29

McErvale, Megan. "Custom protein surfaces for biosensors." Materials Today 12, no. 7-8 (2009): 64. http://dx.doi.org/10.1016/s1369-7021(09)70216-0.

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30

Goetze, T., and J. Brickmann. "Self similarity of protein surfaces." Biophysical Journal 61, no. 1 (1992): 109–18. http://dx.doi.org/10.1016/s0006-3495(92)81820-9.

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31

Baldacci, L., M. Golfarelli, A. Lumini, and S. Rizzi. "Clustering techniques for protein surfaces." Pattern Recognition 39, no. 12 (2006): 2370–82. http://dx.doi.org/10.1016/j.patcog.2006.02.024.

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32

Takami, Yoshiyuki, Shingo Yamane, Kenzo Makinouchi, et al. "Protein adsorption onto ceramic surfaces." Journal of Biomedical Materials Research 40, no. 1 (1998): 24–30. http://dx.doi.org/10.1002/(sici)1097-4636(199804)40:1<24::aid-jbm3>3.0.co;2-t.

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33

Pizzi, Elisabetta, Riccardo Cortese, and Anna Tramontane. "Mapping epitopes on protein surfaces." Biopolymers 36, no. 5 (1995): 675–80. http://dx.doi.org/10.1002/bip.360360513.

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34

Malmsten, Martin. "Protein Adsorption at Phospholipid Surfaces." Journal of Colloid and Interface Science 172, no. 1 (1995): 106–15. http://dx.doi.org/10.1006/jcis.1995.1231.

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35

Kothari, S., P. V. Hatton, and C. W. I. Douglas. "Protein adsorption to titania surfaces." Journal of Materials Science: Materials in Medicine 6, no. 12 (1995): 695–98. http://dx.doi.org/10.1007/bf00134303.

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36

Caelen, Isabelle, Hui Gao, and Hans Sigrist. "Protein Density Gradients on Surfaces." Langmuir 18, no. 7 (2002): 2463–67. http://dx.doi.org/10.1021/la0113217.

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37

Chen, Xin, Laura B. Sagle, and Paul S. Cremer. "Urea Orientation at Protein Surfaces." Journal of the American Chemical Society 129, no. 49 (2007): 15104–5. http://dx.doi.org/10.1021/ja075034m.

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38

Aggarwal, Nitesh, Ken Lawson, Matthew Kershaw, Robert Horvath, and Jeremy Ramsden. "Protein adsorption on heterogeneous surfaces." Applied Physics Letters 94, no. 8 (2009): 083110. http://dx.doi.org/10.1063/1.3078397.

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39

Kirby, Anthony J., Florian Hollfelder, and Dan S. Tawfik. "Nonspecific Catalysis By Protein Surfaces." Applied Biochemistry and Biotechnology 83, no. 1-3 (2000): 173–82. http://dx.doi.org/10.1385/abab:83:1-3:173.

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40

Wahlgren, M. "Protein adsorption to solid surfaces." Trends in Biotechnology 9, no. 1 (1991): 201–8. http://dx.doi.org/10.1016/0167-7799(91)90064-o.

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41

Duncan, Bruce, and Arthur Olson. "Shape analysis of protein surfaces." Journal of Molecular Graphics 10, no. 1 (1992): 50. http://dx.doi.org/10.1016/0263-7855(92)80028-c.

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42

Kato, Koichi, Shushi Sano, and Yoshito Ikada. "Protein adsorption onto ionic surfaces." Colloids and Surfaces B: Biointerfaces 4, no. 4 (1995): 221–30. http://dx.doi.org/10.1016/0927-7765(94)01172-2.

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43

Claesson, Per M., Eva Blomberg, Johan C. Fröberg, Tommy Nylander, and Thomas Arnebrant. "Protein interactions at solid surfaces." Advances in Colloid and Interface Science 57 (May 1995): 161–227. http://dx.doi.org/10.1016/0001-8686(95)00241-h.

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44

Morozova, Olga V., Olga N. Volosneva, Olga A. Levchenko, Nikolay A. Barinov, and Dmitry V. Klinov. "Protein Corona on Gold and Silver Nanoparticles." Materials Science Forum 936 (October 2018): 42–46. http://dx.doi.org/10.4028/www.scientific.net/msf.936.42.

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Gold or silver nanoparticles (NP) were covered with protein corona by: 1) direct binding with a number of proteins; 2) nanoprecipitation of proteins from their solutions in fluoroalcohols; 3) physisorption of proteins on the NP surface treated with poly (allylamine) s; 4) encapsulation of Ag or Au NP into SiO2 envelope and functionalization with organosilanes. Adsorption of proteins on surfaces of metal NP is reversible and up to 70% of the attached proteins can be eluted. Ag NP possess high affinity for binding with immunoglobulins and fibrinogens but not with any protein. Nanoprecipitation o

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45

Fletcher, Steven, and Andrew D. Hamilton. "Targeting protein–protein interactions by rational design: mimicry of protein surfaces." Journal of The Royal Society Interface 3, no. 7 (2006): 215–33. http://dx.doi.org/10.1098/rsif.2006.0115.

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Protein–protein interactions play key roles in a range of biological processes, and are therefore important targets for the design of novel therapeutics. Unlike in the design of enzyme active site inhibitors, the disruption of protein–protein interactions is far more challenging, due to such factors as the large interfacial areas involved and the relatively flat and featureless topologies of these surfaces. Nevertheless, in spite of such challenges, there has been considerable progress in recent years. In this review, we discuss this progress in the context of mimicry of protein surfaces: targ

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46

Penna, Matthew, Kamron Ley, Shane Maclaughlin, and Irene Yarovsky. "Surface heterogeneity: a friend or foe of protein adsorption – insights from theoretical simulations." Faraday Discussions 191 (2016): 435–64. http://dx.doi.org/10.1039/c6fd00050a.

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A lack in the detailed understanding of mechanisms through which proteins adsorb or are repelled at various solid/liquid interfaces limits the capacity to rationally design and produce more sophisticated surfaces with controlled protein adsorption in both biomedical and industrial settings. To date there are three main approaches to achieve anti biofouling efficacy, namely chemically adjusting the surface hydrophobicity and introducing various degrees of surface roughness, or a combination of both. More recently, surface nanostructuring has been shown to have an effect on protein adsorption. H

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47

REDDY, BOOJALA V. B., and YIANNIS N. KAZNESSIS. "A QUANTITATIVE ANALYSIS OF INTERFACIAL AMINO ACID CONSERVATION IN PROTEIN-PROTEIN HETERO COMPLEXES." Journal of Bioinformatics and Computational Biology 03, no. 05 (2005): 1137–50. http://dx.doi.org/10.1142/s0219720005001429.

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A long-standing question in molecular biology is whether interfaces of protein-protein complexes are more conserved than the rest of the protein surfaces. Although it has been reported that conservation can be used as an indicator for predicting interaction sites on proteins, there are recent reports stating that the interface regions are only slightly more conserved than the rest of the protein surfaces, with conservation signals not being statistically significant enough for predicting protein-protein binding sites. In order to properly address these controversial reports we have studied a s

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48

Friedman, J. M. "Fourier-filtered van der Waals contact surfaces: accurate ligand shapes from protein structures." Protein Engineering Design and Selection 10, no. 8 (1997): 851–63. http://dx.doi.org/10.1093/protein/10.8.851.

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49

Yang, Yu, Steffen Knust, Sabrina Schwiderek, et al. "Protein Adsorption at Nanorough Titanium Oxide Surfaces: The Importance of Surface Statistical Parameters beyond Surface Roughness." Nanomaterials 11, no. 2 (2021): 357. http://dx.doi.org/10.3390/nano11020357.

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The nanoscale surface topography of biomaterials can have strong effects on protein adsorption. While there are numerous surface statistical parameters for the characterization of nanorough surfaces, none of them alone provides a complete description of surface morphology. Herein, a selection of nanorough titanium oxide surfaces has been fabricated with root-mean-square roughness (Sq) values below 2.7 nm but very different surface morphologies. The adsorption of the proteins myoglobin (MGB), bovine serum albumin (BSA), and thyroglobulin (TGL) at these surfaces was investigated in situ by ellip

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50

SHINDO, Heisaburo. "Biological Surfaces. Environment of Protein Surface Studied by NMR Spectroscopy." Journal of the Surface Finishing Society of Japan 45, no. 2 (1994): 143–51. http://dx.doi.org/10.4139/sfj.45.143.

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