Sequence Effects on Peptide Assembly Characteristics Observed by Using Scanning Tunneling Microscopy

Mao, Xiaobo; Guo, Yuanyuan; Luo, Yin; Lin, Na; Liu, Lei; Ma, Xiang; Wang, Huibin; Yang, Yan; Wei, Guanghong; Wang, Chen

doi:10.1021/ja307198u

Cited by 48 publications

(45 citation statements)

References 23 publications

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“…171 In particular, they studied the behavior of two synthetic model peptides, namely R 4 G 4 H 8 and F 4 G 4 H 8 , adsorbed onto HOPG by STM images and rationalized the experimental evidences with theoretical studies. 171 In particular, they studied the behavior of two synthetic model peptides, namely R 4 G 4 H 8 and F 4 G 4 H 8 , adsorbed onto HOPG by STM images and rationalized the experimental evidences with theoretical studies.…”

Section: Graphene and Proteinsmentioning

confidence: 95%

Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies

2015

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This critical review aims at giving insights on the spontaneous tendency of proteins and their constitutive parts to adsorb on graphitic nanomaterials (GNMs) through non-covalent interactions occurring at their interfaces. Specifically, it focuses on the theoretical and experimental studies carried out to comprehend in depth the forces ruling the adsorption processes of proteins on fullerene, carbon nanotubes and graphene. In a systematic way the reader is guided through the most recent and representative examples describing at the atomistic level of detail the structural modalities and the chemico-physical principles through which amino acids, polypeptides and folded proteins interact with GNMs' surface, thereby taking into consideration the mutual effects of both protein structural complexity and nanomaterial topology. Based on their chemical and structural features, the study and understanding of the protein-nanomaterial interfaces can be exploited in the view of design and control the spontaneous formation of biologically-active hybrid materials for the development of new tailored applications in the field of sensing, nanomedicine and biochemistry.

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Section: Graphene and Proteinsmentioning

confidence: 95%

Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies

2015

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“…Microscopy has been used to observe the structure of adsorbed peptides at graphitic interfaces under dry conditions. [12][13][14] However, the relationship between the interfacial structure of peptides when dried, vs. in-solution conditions is not yet understood; it is highly likely that the drying process strongly affects the resulting packing morphology of the adsorbed chains. Existing structural data obtained for peptides adsorbed at aqueous interfaces are often (but not always) based on indirect techniques such as circular dichroism spectroscopy, 13,15 although advances have been made in for insolution NMR in the adsorbed state.…”

Section: Introductionmentioning

confidence: 99%

What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces

2015

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Investigation of the non-covalent interaction of biomolecules with aqueous graphene interfaces is a rapidly expanding area. However, reliable exploitation of these interfaces in many applications requires that the links between the sequence and binding of the adsorbed peptide structures be clearly established. Molecular dynamics (MD) simulations can play a key role in elucidating the conformational ensemble of peptides adsorbed at graphene interfaces, helping to elucidate these rules in partnership with experimental characterisation. We apply our recently-developed polarisable force-field for biomolecule-graphene interfaces, GRAPPA, in partnership with advanced simulation approaches, to probe the adsorption behaviour of peptides at aqueous graphene. First we determine the free energy of adsorption of all twenty naturally occurring amino acids (AAs) via metadynamics simulations, providing a benchmark for interpreting peptide-graphene adsorption studies. From these free energies, we find that strong-binding amino acids have flat and/or compact side chain groups, and we relate this behaviour to the interfacial solvent structuring. Second, we apply replica exchange with solute tempering simulations to efficiently and widely sample the conformational ensemble of two experimentally-characterised peptide sequences, P1 and its alanine mutant P1A3, in solution and adsorbed on graphene. For P1 we find a significant minority of the conformational ensemble possesses a helical structure, both in solution and when adsorbed, while P1A3 features mostly extended, random-coil conformations. In solution this helical P1 configuration is stabilised through favourable intra-peptide interactions, while the adsorbed structure is stabilised via interaction of four strongly-binding residues, identified from our metadynamics simulations, with the aqueous graphene interface. Our findings rationalise the performance of the P1 sequence as a known graphene binder.

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“…Such effect of phosphorylation on the intrinsic propensity toward certain local backbone conformations can be especially important for intrinsically disordered proteins, for which the long-range global interactions are less significant compared to those of well-structured proteins. In addition, the intrinsic propensity toward certain local backbone conformations of a certain amino acid is also an important input for some computational models of protein folding/aggregation and structure predictions [11][12][13][14][15][16][17]. For example, recent computational works showed that introducing amino acid-specific parameters to the intrinsic conformational propensity in the all-atom force field can drastically improve protein folding and structure predictions [18,19].…”

Section: Introductionmentioning

confidence: 99%

Effects of phosphorylation on the intrinsic propensity of backbone conformations of serine/threonine

Gao

Zhang

et al. 2016

J Biol Phys

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Each amino acid has its intrinsic propensity for certain local backbone conformations, which can be further modulated by the physicochemical environment and post-translational modifications. In this work, we study the effects of phosphorylation on the intrinsic propensity for different local backbone conformations of serine/threonine by molecular dynamics simulations. We showed that phosphorylation has very different effects on the intrinsic propensity for certain local backbone conformations for the serine and threonine. The phosphorylation of serine increases the propensity of forming polyproline II, whereas that of threonine has the opposite effect. Detailed analysis showed that such different responses to phosphorylation mainly arise from their different perturbations to the backbone hydration and the geometrical constraints by forming sidechain-backbone hydrogen bonds due to phosphorylation. Such an effect of phosphorylation on backbone conformations can be crucial for understanding the molecular mechanism of phosphorylation-regulated protein structures/dynamics and functions.

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Sequence Effects on Peptide Assembly Characteristics Observed by Using Scanning Tunneling Microscopy

Cited by 48 publications

References 23 publications

Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies

Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies

What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces

Effects of phosphorylation on the intrinsic propensity of backbone conformations of serine/threonine

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