Exploring the Changes in the Structure of α-Helical Peptides Adsorbed onto a Single Walled Carbon Nanotube Using Classical Molecular Dynamics Simulation

Balamurugan, Kanagasabai; Gopalakrishnan, R; Raman, Srivatsan; Subramanian, V.

doi:10.1021/jp106177n

Cited by 54 publications

(74 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To alter the hydrophobicity, surface modifications with surface defects and polar groups have been suggested, but these affect the stability of the materials as well as their mechanical and electrical properties (Scida et al 2011). Computational studies of protein-carbon surface interactions have mostly focused on graphene/graphite (Mereghetti & Wade, 2011;Mücksch & Urbassek, 2011;Raffaini & Ganazzoli, 2010;Kang et al 2013;Sun et al 2014b;Yu et al 2012b), CNT (Balamurugan et al 2010;Chen et al 2009b;Tallury & Pasquinelli, 2010;Wang et al 2003) and fullerenes (Durdagi et al 2008;Kraszewski et al 2010;Noon et al 2002).…”

Section: Carbon Allotropesmentioning

confidence: 99%

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

197

199

View full text Add to dashboard Cite

Abstract. Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time-and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.

show abstract

Section: Carbon Allotropesmentioning

confidence: 99%

Modeling and simulation of protein–surface interactions: achievements and challenges

Ozboyaci

Kokh

Corni

et al. 2016

Quart. Rev. Biophys.

197

199

View full text Add to dashboard Cite

show abstract

“…Adhered Gd@C 82 (OH) 22 can enhance the stability of native triple helical structure of tropocollagen and facilitate the protein assembly. Interestingly, the interaction of nanoparticle with protein was often considered to disturb protein structure or induce abnormal assembly, [47][48][49][50] while, as indicated in our work, nanoparticle may also enhance the native structure and assembly of protein.…”

Section: Fullerene Derivative Gd@c 82 (Oh) 22mentioning

confidence: 53%

Computational studies on the interactions of nanomaterials with proteins and their impacts

An¹,

Su²,

Li³

et al. 2015

Chinese Phys. B

View full text Add to dashboard Cite

Intensive concerns about the biosafety of nanomaterials demand the systematic study of the mechanisms about their biological effects. Many biological effects can be attributed to the interaction of nanomaterials with protein and their impacts on protein function. On the other hand, nanomaterials exhibit the potential in a variety of biomedical applications, many of which also involve the direct interaction with protein. In this paper, we review some recent computational studies about this subject, especially the interaction of carbon and gold nanomaterials. Besides the hydrophobic and π-stacking interactions, the interaction mode of carbon nanomaterials can be regulated by their functional groups. And the coating of gold nanomaterials also adjusts their interaction mode, in addition to the coordination interaction with cysteine's sulfur group and histidine's imidazole group. Moreover, nanomaterials can interact with multiple proteins and the impacts on protein activity are attributed to a wide spectrum of mechanisms. The findings about the mechanisms of nanomaterial-protein interaction can further guide the design and development of nanomaterial to realize the applications in disease diagnosis and treatment.

show abstract

“…For instance, both carbon nanotubes and graphene have been shown to distort the α-helical structures of peptides [32,33], but with graphene exhibiting much higher impact since it has more favorable surface curvature [35] for binding with protein residues such as tryptophan [31]. In this section, we discuss graphene's interaction with protein using villin headpiece (HP35) as an example.…”

Section: Graphene Disruption To Protein Structure and Functionmentioning

confidence: 99%

“…Meanwhile, the recent molecular dynamics (MD) simulations of proteins, DNAs, and cell membranes interacting with graphene nanosheets have also shed light on this challenging problem [29][30][31]. Graphene displays stronger capability in disrupting protein structures than carbon nanotubes and fullerenes [32][33][34] due to its more favorable surface curvature [34,35] and stronger π-π stacking interactions [31]. This chapter will go over some of the recent advances in this new research area by illustrating a few interesting topics in more detail that have captivated an array of researchers from different perspectives.…”

mentioning

confidence: 99%

Graphene and Derivatives

Zhou

2015

Modeling of Nanotoxicity

View full text Add to dashboard Cite

As mentioned in the previous two chapters, the increased use of nanomaterials in biomedicine has also created keen interest in exploring their interactions with tissues, cells, and biomolecules [1]. A detailed understanding of how nanomaterials interact with biomolecules at the molecular level is essential to the safe usage of nanoparticle-based biomedical technologies [2][3][4][5][6][7][8]. Recently, the interactions between proteins, nucleic acids (such as DNA), and cell membranes with nanomaterials (particularly, graphitic nanomaterials) have been studied extensively using experiments and simulations, and they have been shown to affect both the structure and function of biological systems, resulting in serious cytotoxicity and biosafety concerns.Compared to 0D fullerenes (see Chap. 2) and 1D carbon nanotubes (see Chap. 3), the interactions between 2D graphene nanosheets with biomolecules and the resulting cytotoxicity are much less studied. Graphene is a flat monolayer of carbon atoms arranged in a two-dimensional hexagonal lattice [9][10][11], which can be used as the basic building block for fullerenes, carbon nanotubes (CNTs), and graphite. Since its first isolation in a stable form in 2004, graphene has attracted worldwide research interests in the fields of nanoscience and nanotechnology due to its unique structural, mechanical, and electronic properties, and has shortly become the subject of the 2010 Nobel Prize in Physic. In the field of biomedical applications, the high specific surface area of graphene provides a major advantage as it allows high-density bio-functionalization, which is essential for nanotechnology-based drug delivery [12][13][14][15][16]. Titov et al. [17] performed coarse-grained molecular dynamics simulations to study the interaction of few-layer graphene (FLG) nanosheets with a lipid bilayer and reported stable graphene-lipid hybrid structures. Guo et al. [18] and Wang et al. [19] worked on the translocation of small graphene nanosheets across lipid bilayers. The smooth, continuous topography and biopersistence of graphene play a unique role in its foreign-body-induced carcinogenesis and tumor progression studies [20,21].

show abstract

Exploring the Changes in the Structure of α-Helical Peptides Adsorbed onto a Single Walled Carbon Nanotube Using Classical Molecular Dynamics Simulation

Cited by 54 publications

References 66 publications

Modeling and simulation of protein–surface interactions: achievements and challenges

Modeling and simulation of protein–surface interactions: achievements and challenges

Computational studies on the interactions of nanomaterials with proteins and their impacts

Graphene and Derivatives

Contact Info

Product

Resources

About