The structure difference of proteins isolated on substrate with different techniques as studied by the atomic force microscope

Umemura, Kazuo; Sutoh, Kazuo; Tokunaga, Fumio; Kataoka, Mikio; Kamkubo, H.; Arakawa, Hideo; Ikai, Atsushi

doi:10.1002/sca.1996.4950180403

Cited by 6 publications

(6 citation statements)

References 36 publications

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“…Although our model may require further refinement for predicting the lateral dimension, it is not clear how accurate the lateral dimension predicted from SV analysis is because a cylinder may not correctly approximate the sedimentation or diffusion behavior of a supercoiling rod. For AFM, the heights of protein structures are consistently smaller than the expected diameters of such structures in solution (26,27). Here, we suggest that interactions with the mica surface might cause a partial collapse of the suprahelical structure, which, when combined with forces exerted by the AFM tip to compress the material (Fig.…”

Section: Resultsmentioning

confidence: 57%

Toward the development of peptide nanofilaments and nanoropes as smart materials

Wagner

Phillips

Ali

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

119

117

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Protein design studies using coiled coils have illustrated the potential of engineering simple peptides to self-associate into polymers and networks. Although basic aspects of self-assembly in protein systems have been demonstrated, it remains a major challenge to create materials whose large-scale structures are well determined from design of local protein-protein interactions. Here, we show the design and characterization of a helical peptide, which uses phased hydrophobic interactions to drive assembly into nanofilaments and fibrils (''nanoropes''). Using the hydrophobic effect to drive self-assembly circumvents problems of uncontrolled self-assembly seen in previous approaches that used electrostatics as a mode for self-assembly. The nanostructures designed here are characterized by biophysical methods including analytical ultracentrifugation, dynamic light scattering, and circular dichroism to measure their solution properties, and atomic force microscopy to study their behavior on surfaces. Additionally, the assembly of such structures can be predictably regulated by using various environmental factors, such as pH, salt, other molecular crowding reagents, and specifically designed ''capping'' peptides. This ability to regulate self-assembly is a critical feature in creating smart peptide biomaterials.biomaterial ͉ coiled coil ͉ protein design ͉ circular dichroism ͉ atomic force microscopy D esigned proteins are valuable paradigms for engineering at the nanoscale, offering favorable properties such as atomiclevel precision and tight regulation of self-assembly by using a variety of environmental cues (i.e., pH, ionic strength, temperature) (1-3). As one of the most well studied and naturally abundant structural motifs in proteins, coiled coils are particularly suited to protein design. Their basic sequence feature, the heptad repeat, is a seven-residue pattern (abcdefg) n of nonpolar and polar residues that gives rise to amphipathic ␣-helices. The hydrophobic effect drives the burial of nonpolar residues at the helix-pairing interface and influences geometric details of resulting structures (4). Electrostatic and polar residues at buried or solvent-exposed locations provide additional means to manipulate structural features by stabilization or destabilization (negative design) of key interactions (5-8).Recent attempts to design self-assembling protein networks by using coiled coils have focused on simple systems, such as linear and branched fibrils (9-14), planar assemblies (15), and hydrogels (16-18). Specifically, filament formation has been achieved by stabilization of intermediate structures that foster intermolecular coiled-coil interactions (11)(12)(13)(14). Previous studies have reported the design of short helical peptides, which interact via a dimeric coiled-coil motif and are stabilized by a combination of overlapping hydrophobic and electrostatic intermolecular interactions (9, 13, 14). These peptides do indeed self-assemble into filaments; however, these filaments also show evidence of extensive...

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Section: Resultsmentioning

confidence: 57%

Toward the development of peptide nanofilaments and nanoropes as smart materials

Wagner

Phillips

Ali

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

119

117

View full text Add to dashboard Cite

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“…How are results obtained on TMV generalizable to other biomolecules? Size reduction in molecular height has been detected with AFM for a long time (Umemura et al, 1996). The origin of such a reduction in height has been attributed mostly to high-force when imaging and to substrates.…”

Section: Discussionmentioning

confidence: 99%

“…Results on lysozyme and carbonic anhydrase II revealed the viscoelastic property of single proteins under indentation, but without noticing full denaturation (Radmacher et al, 1994;Afrin et al, 2005). Nevertheless, numerous studies demonstrated difficulties in obtaining accurate topography of biomolecules such as proteins (Umemura et al, 1996;Bergkvist et al, 1998;Cheung and Walker, 2008) and nucleic acids (Moreno-Herrero et al, 2003;Yang et al, 2007). To fully exploit the capacity of AFM to produce high resolution topographical surfaces of single biomolecules, as required in three-dimensional atomic reconstruction (Czajkowsky and Shao, 2009;Trinh et al, 2012;Chaves et al, 2014;He et al, 2016), it is critical to evaluate all sources of errors in topographical surface measurement accuracy.…”

Section: Introductionmentioning

confidence: 99%

Conditions to minimize soft single biomolecule deformation when imaging with atomic force microscopy

Godon

Teulon

Odorico

et al. 2017

Journal of Structural Biology

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A recurrent interrogation when imaging soft biomolecules using atomic force microscopy (AFM) is the putative deformation of molecules leading to a bias in recording true topographical surfaces. Deformation of biomolecules comes from three sources: sample instability, adsorption to the imaging substrate, and crushing under tip pressure. To disentangle these causes, we measured the maximum height of a well-known biomolecule, the tobacco mosaic virus (TMV), under eight different experimental conditions positing that the maximum height value is a specific indicator of sample deformations. Six basic AFM experimental factors were tested: imaging in air (AIR) versus in liquid (LIQ), imaging with flat minerals (MICA) versus flat organic surfaces (self-assembled monolayers, SAM), and imaging forces with oscillating tapping mode (TAP) versus PeakForce tapping (PFT). The results show that the most critical parameter in accurately measuring the height of TMV in air is the substrate. In a liquid environment, regardless of the substrate, the most critical parameter is the imaging mode. Most importantly, the expected TMV height values were obtained with both imaging with the PeakForce tapping mode either in liquid or in air at the condition of using self-assembled monolayers as substrate. This study unambiguously explains previous poor results of imaging biomolecules on mica in air and suggests alternative methodologies for depositing soft biomolecules on well organized self-assembled monolayers.

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“…It is obvious that a hard and highly charged mineral substrate (such as mica) creates difficulties during the adsorption of molecules on which they tend to partially denature (Umemura et al, 1996). However, softer systems for depositing molecules such as functionalized self-assembled monolayers are emerging (Lv et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

Computational Reconstruction of Multidomain Proteins Using Atomic Force Microscopy Data

et al. 2012

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Summary Classical structural biology techniques face a great challenge to determine the structure at the atomic level of large and flexible macromolecules. We present a novel methodology that combines high-resolution AFM topographic images with atomic coordinates of proteins to assemble very large macromolecules or particles. Our method uses a two-step protocol: atomic coordinates of individual domains are docked beneath the molecular surface of the large macromolecule, and then each domain is assembled using a combinatorial search. The protocol was validated on three test cases: a simulated system of antibody structures; and two experimentally-based test cases: Tobacco mosaic virus, a rod-shaped virus; and aquaporin Z, a bacterial membrane protein. We have shown that AFM-intermediate resolution topography and partial surface data are useful constraints for building macromolecular assemblies. The protocol is applicable to multi-component structures connected in the polypeptide chain or as disjoint molecules. The approach effectively increases the resolution of AFM beyond topographical information down to atomic-detail structures.

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The structure difference of proteins isolated on substrate with different techniques as studied by the atomic force microscope

Cited by 6 publications

References 36 publications

Toward the development of peptide nanofilaments and nanoropes as smart materials

Toward the development of peptide nanofilaments and nanoropes as smart materials

Conditions to minimize soft single biomolecule deformation when imaging with atomic force microscopy

Computational Reconstruction of Multidomain Proteins Using Atomic Force Microscopy Data

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