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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 (February 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 presence of hydrophobic surfaces, SOD1 unfolding promotes fibril nucleation. By contrast, in the presence of hydrophilic surfaces, increasing denaturant concentration retards the onset of fibril formation. We conclude that the mechanism of fibril formation depends on the surrounding surfaces and that the nucleating species might correspond to different conformational states of SOD1 depending on the nature of these surfaces.

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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 (December 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 surface motifs is extracted in this phase, making it difficult to distinguish whether the extracted motifs are significant to be considered active sites. Since active sites from proteins with a particular function have similar shape and physical properties, proteins can be classified based on similarity among local surfaces. Thus, in the filtering phase, local surfaces extracted from proteins of the same group are considered significant motifs, and the rest are filtered out. The proposed method was applied to discover surface motifs from 15 proteins belonging to four function groups. Motifs corresponding to all 4 known functional sites were recognised.

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3

Znamenskiy, Denis, Khan Le Tuan, Anne Poupon, Jacques Chomilier, and Jean-Paul Mornon. "β-Sheet modeling by helical surfaces." Protein Engineering, Design and Selection 13, no. 6 (June 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 (June 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 (July 30, 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 electrochemical approach to determining the folding free energy of proteins site-specifically attached to chemically well-defined, macroscopic surfaces. Comparison with the folding free energies seen in bulk solution then provides a quantitative measure of the extent to which surface interactions alter protein stability. As proof-of-principle, we have characterized the FynSH3 domain site-specifically attached to a hydroxyl-coated surface. Upon guanidinium chloride denaturation, the protein unfolds in a reversible, two-state manner with a free energy within 2 kJ/mol of the value seen in bulk solution. Assuming that excluded volume effects stabilize surface-attached proteins, this observation suggests there are countervening destabilizing interactions with the surface that, under these conditions, are similar in magnitude. Our technique constitutes an unprecedented experimental tool with which to answer long-standing questions regarding the molecular-scale origins of protein−surface interactions and to facilitate rational optimization of surface biocompatibility.

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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 (May 2006): 361–78. http://dx.doi.org/10.1145/1147954.1147957.

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7

Lehnfeld, J., Y. Dukashin, J. Mark, G. D. White, S. Wu, V. Katzur, R. Müller, and S. Ruhl. "Saliva and Serum Protein Adsorption on Chemically Modified Silica Surfaces." Journal of Dental Research 100, no. 10 (June 22, 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 biomaterial surface, we have measured the amount of protein adsorbed and analyzed the composition of the adsorbed protein layer using gel electrophoresis and western blotting. Here, we have developed an in vitro model system based on silica surfaces, chemically modified with 7 silane-based self-assembled monolayers that span a broad range of physicochemical properties, from hydrophilic to hydrophobic surfaces (water contact angles from 15° to 115°), low to high surface free energy (12 to 57 mN/m), and negative to positive surface charge (zeta potentials from –120 to +40 mV at physiologic pH). We found that the chemical surface functionalities exerted a substantial effect on the total amounts of proteins adsorbed; however, no linear correlation of the adsorbed amounts with the physicochemical surface parameters was observed. Only the adsorption behavior of a few singular protein components, from which physicochemical data are available, seems to follow physicochemical expectations. Examples are albumin in serum and lysozyme in saliva; in both, adsorption was favored on countercharged surfaces. We conclude from these findings that in complex biofluids such as saliva and serum, adsorption behavior is dominated by the overall protein-binding capacity of the surface rather than by specific physicochemical interactions of single protein entities with the surface.

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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 (May 28, 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 nanostructure of a block copolymer can be controlled by manipulating the chemistry and arrangement of the blocks. Random, A–B and A–B–A block copolymers composed of methyl methacrylate copolymerized with either acrylic acid or 2-hydroxyethyl methacrylate will be explored. Using atomic force microscopy (AFM), the surface morphology of these block copolymers will be characterized. Further, AFM tips functionalized with proteins will measure the adhesion of that particular protein to polymer surfaces. In this manner, the influence of block copolymer morphology on protein adhesion can be measured. AFM tips functionalized with antibodies to fibronectin will determine how the surfaces will affect the conformation of fibronectin, an important parameter in evaluating surface biocompatibility.

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9

Wach, Jean-Yves, Barbora Malisova, Simone Bonazzi, Samuele Tosatti, Marcus Textor, Stefan Zürcher, and Karl Gademann. "Protein-Resistant Surfaces through Mild Dopamine Surface Functionalization." Chemistry - A European Journal 14, no. 34 (October 16, 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, Vojko Vlachy, Robert G. Bryant, Guillaume Mériguet, Natalie Malikova, and Anne-Laure Rollet. "Multiscale Water Dynamics on Protein Surfaces: Protein-Specific Response to Surface Ions." Journal of Physical Chemistry B 125, no. 31 (August 3, 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 (July 1, 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 serum albumin (BSA) with both SiO2 surfaces to create a monolayer of coating protein was studied. Subsequently, the interaction of these BSA-coated surfaces with a non-ionic surfactant (a decanol ethoxylated with an average number of eight ethoxy groups) was investigated. A fair comparison between the results obtained by these two techniques on different geometries required the correction of SPR data for bound water and DLS results for particle curvature. Thus, the treated data have excellent quantitative agreement independently of the geometry of the surface suggesting the formation of multilayers of C10PEG over the protein coating. The results also show a marked different affinity of the surfactant towards BSA when the protein is deposited on a flat surface or individually dissolved in solution.

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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 (August 4, 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 (January 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 dislodged, thus causing loss of signal. They also result in random attachment of the protein to the surface. Site–specific covalent attachment of proteins onto surfaces, on the other hand, leads to molecules being arranged in a definite, orderly fashion and uses spacers and linkers to help minimize steric hindrances between the protein and the surface. This work reviews in detail some of the methods most commonly used as well as the latest developments for the site-specific covalent attachment of protein to solid surfaces.

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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 (April 6, 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 (March 24, 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 years about protein adsorption on titanium-based materials is reviewed. How the surface characteristics affect protein adsorption is investigated, aiming to provide an as comprehensive a picture as possible of adsorption mechanisms and type of chemical bonding with the surface, as well as of the characterization techniques effectively applied to model and real implant surfaces. Surface free energy, charge, microroughness, and hydroxylation degree have been found to be the main surface parameters to affect the amount of adsorbed proteins. On the other hand, the conformation of adsorbed proteins is mainly dictated by the protein structure, surface topography at the nano-scale, and exposed functional groups. Protein adsorption on titanium surfaces still needs further clarification, in particular concerning adsorption from complex protein solutions. In addition, characterization techniques to investigate and compare the different aspects of protein adsorption on different surfaces (in terms of roughness and chemistry) shall be developed.

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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 nano-wrinkled surfaces is studied through Monte Carlo simulations. The wrinkled surface is modeled by a sinusoidal surface. Free-energy barriers for heterogeneous crystal nucleation on flat and wrinkled surfaces are computed and compared. The study reveals that the enhancement of nucleation is closely related to the two step nucleation process seen during protein crystallization. There is an enhancement of protein concentration near the trough of the sinusoidal surface which aids in nucleation. However, the high curvature at the trough acts as a deterrent to crystal nucleus formation. Hence, significant lowering of the free-energy barrier is seen only if the increase in the protein concentration at the trough is very high.

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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 (December 1, 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 (December 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 (April 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 (September 6, 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 (July 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 (January 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 investigate how they distribute and cluster among the ESOM map. They obtained 30-50 clusters of local surfaces of different characteristics, which will be useful for annotating surface of proteins.

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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 (June 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 (October 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 (February 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 (July 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 (January 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 (December 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, Goro Otsuka, Julie Glueck, Robert Benkowski, and Yukihiko Nos�. "Protein adsorption onto ceramic surfaces." Journal of Biomedical Materials Research 40, no. 1 (April 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 (November 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 (June 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 (December 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 (April 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 (December 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 (February 23, 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 (January 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 (March 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 (May 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 of Ag and Au NP with proteins resulted in combined NP with metal core and protein shell with ligand-binding and enzymatic activities. SiO2 layer on surfaces of metal NP is suitable for silanization and covalent immobilization of any protein. Protein corona prevents Ag and Au NP from oxidation, dissolution and aggregation. Proteins attached to metal NP reduce their antimicrobial activity and cytotoxicity for eukaryotic cells. The developed methods of fabrication of Ag/Au NP with protein shells permit to attach any protein at different distances from metal core to avoid possible inactivation of proteins, to reduce fluorescence fading and to stabilize the nanoconjugates.

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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 (March 8, 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: targeting protein–protein interactions by rational design.

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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. However, the current resolution of experimental techniques makes it difficult to investigate these three phase systems at the molecular level. In this molecular dynamics study we explore in all-atom detail the adsorption process of one of the most surface active proteins, EAS hydrophobin, known for its versatile ability to self-assemble on both hydrophobic and hydrophilic surfaces forming stable monolayers that facilitate further biofilm growth. We model the adsorption of this protein on organic ligand protected silica surfaces with varying degrees of chemical heterogeneity and roughness, including fully homogenous hydrophobic and hydrophilic surfaces for comparison. We present a detailed characterisation of the functionalised surface structure and dynamics for each of these systems, and the effect the ligands have on interfacial water, the adsorption process and conformational rearrangements of the protein. Results suggest that the ligand arrangement that produces the highest hydrophilic chain mobility and the lack of significant hydrophobic patches shows the most promising anti-fouling efficacy toward hydrophobin. However, the presence on the protein surface of a flexible loop with amphipathic character (the Cys3–Cys4 loop) is seen to facilitate EAS adsorption on all surfaces by enabling the protein to match the surface pattern.

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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 (October 2005): 1137–50. http://dx.doi.org/10.1142/s0219720005001429.

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Abstract:

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 set of 28 well resolved hetero complex structures of proteins that consists of transient and non-transient complexes. The surface positions were classified into four conservation classes and the conservation index of the surface positions was quantitatively analyzed. The results indicate that the surface density of highly conserved positions is significantly higher in the protein-protein interface regions compared with the other regions of the protein surface. However, the average conservation index of the patches in the interface region is not significantly higher compared with other surface regions of the protein structures. This finding demonstrates that the number of conserved residue positions is a more appropriate indicator for predicting protein-protein binding sites than the average conservation index in the interacting region. We have further validated our findings on a set of 59 benchmark complex structures. Furthermore, an analysis of 19 complexes of antigen-antibody interactions shows that there is no conservation of amino acid positions in the interacting regions of these complexes, as expected, with the variable region of the immunoglobulins interacting mostly with the antigens. Interestingly, antigen interacting regions also have a higher number of non-conserved residue positions in the interacting region than the rest of the protein surface.

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Friedman, J. M. "Fourier-filtered van der Waals contact surfaces: accurate ligand shapes from protein structures." Protein Engineering Design and Selection 10, no. 8 (August 1, 1997): 851–63. http://dx.doi.org/10.1093/protein/10.8.851.

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Yang, Yu, Steffen Knust, Sabrina Schwiderek, Qin Qin, Qing Yun, Guido Grundmeier, and Adrian Keller. "Protein Adsorption at Nanorough Titanium Oxide Surfaces: The Importance of Surface Statistical Parameters beyond Surface Roughness." Nanomaterials 11, no. 2 (February 1, 2021): 357. http://dx.doi.org/10.3390/nano11020357.

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Abstract:

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 ellipsometry to assess the importance of six of the most common surface statistical parameters. For BSA adsorption, both protein film thickness and time constant of adsorption were found to scale linearly with Sq s. For TGL, however, the same adsorption characteristics depend linearly on the surface skewness (Ssk), which we attribute to the rather extreme size of this protein. Finally, a mixed behavior is observed for MGB adsorption, showing different linear correlations with Sq and Ssk. These results demonstrate the importance of a thorough morphological characterization of the surfaces employed in protein adsorption and possibly also cell adhesion studies.

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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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