Estimation of the free energy of adsorption of a polypeptide on amorphous SiO<sub>2</sub>from molecular dynamics simulations and force spectroscopy experiments

Meißner, Robert H.; Wei, Gang; Ciacchi, Lucio Colombi

doi:10.1039/c5sm01444a

Cited by 33 publications

(45 citation statements)

References 77 publications

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“…The stretching of protein barnase by way of optical tweezers gives work values of over 1000 k B T 56 and the authors comment on different contributing factors. A study of short peptide's adsorption on amorphous SiO 2 shows that a friction emerging from pulling a peptide through water contributes to work in a linear way, quickly rising with dragging speed 57 , while maximum work of pulling 18 residue-long pVEC peptide variants through the POPE bilayer has been estimated to be between 797 and 919 kcal/mol 58 . As it is, work values, we have arrived at, are within expectations for this type of simulation.…”

Section: Resultsmentioning

confidence: 99%

Delineating elastic properties of kinesin linker and their sensitivity to point mutations

Świątek

Gudowska–Nowak

2020

Sci Rep

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We analyze free energy estimators from simulation trials mimicking single-molecule pulling experiments on a neck linker of a kinesin motor. For that purpose, we have performed a version of steered molecular dynamics (SMD) calculations. the sample trajectories have been analyzed to derive distribution of work done on the system. In order to induce stretching of the linker, we have applied a constant pulling force to the molecule and allowed for a subsequent relaxation of its structure. the use of fluctuation relations (FR) relevant to non-equilibrium systems subject to thermal fluctuations allows us to assess the difference in free energy between stretched and relaxed conformations. To further understand effects of potential mutations on elastic properties of the linker, we have performed similar in silico studies on a structure formed of a polyalanine sequence (Ala-only) and on three other structures, created by substituting selected types of amino acid residues in the linker's sequence with alanine (Ala) ones. the results of SMD simulations indicate a crucial role played by the Asparagine (Asn) and Lysine (Lys) residues in controlling stretching and relaxation properties of the linker domain of the motor.The motor proteins' ability to generate movement creates a situation, where it is possible to treat different parts of one molecule as linked but functionally separate objects, that possess an ability to move at different times and speeds 1 . That makes the field of motor proteins a desirable testing ground for application of various theoretical models, that aim to filter the inherent complexity of biological systems 2-5 . Among the motors, members of the kinesin protein superfamily are consistently used throughout the years in research focusing on molecular motors' mechanical properties, both in vitro 2 and in silico 2,4-6 .A conformational change of a region within kinesin has been shown to be associated with its movement along microtubule 7 . This region has been labeled as neck linker. The label refers to a concise (less than 20 amino acids length) amino acid sequence in a single kinesin head that acts as a bridge between α-6 helix in coiled-coil dimerization domain and α-7 helix in the core motor domain, respectively 8 . While its exact length as well as the placement within sequence of its N-and C-termini are not set in stone 9 , some of its residue patterns are present across all kinesin families, while neck linker sequences within a single family are very similar 8 . All this suggest that parts of neck linker region have been conserved, which makes neck linker a non-random, specific sequence. An on-going accumulation of experimental data evidence suggests that a transition of the neck linker from a disordered (random coil) state to an ordered (β-sheet) conformation is a key factor in determining a mechanism of force-generation that is a crucial element of molecular motors' ability to move along microtubules 7,8 . Attempts at substituting neck linker with a peptide of a different sequence, as well as exte...

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Section: Resultsmentioning

confidence: 99%

Delineating elastic properties of kinesin linker and their sensitivity to point mutations

Świątek

Gudowska–Nowak

2020

Sci Rep

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“…For instance, Wei et al demonstrated the surface functionalization of AFM Si 3 N 4 tips with a facile method for binding DNA, peptide and proteins for the SMFS determination of the interactions between biomolecules and various materials [22,23,32]. As shown in Figure 1a, the Si 3 N 4 tip was first modified with 3-aminopropyl triethoxysilane (APTES) and thiethoxychorosilane (TTCS) through the silanization to form -NH 2 group on the surface of the tip, which could further react with the bifunctional N-hydroxysuccimidyl (NHS)-PEG-NHS ester disulfide to provide the -NH 2 -binding groups on the tip.…”

Section: Tip Functionalizationmentioning

confidence: 99%

“…Previously, various famous nanomaterials including metallic nanoparticles [15], carbon nanotubes [16], graphene [17], and other two-dimensional nanomaterials [18], have been conjugated with proteins, peptides, DNA/ RNA, enzymes and others for realizing the bio-applications in bionanotechnology, biomedicine and tissue engineering. It is well known that the formation of stable bio-hybrids is based on the interaction forces between biomolecules and the materials interfaces, which could be measured experimentally and theoretically by using some techniques such as optical tweezers and fluorescent spectroscopy [19], calorimetry titration [20], polymerase chain reaction [21], force spectroscopy (FD) [22], and molecular dynamic simulations [23].…”

Section: Introductionmentioning

confidence: 99%

Single-molecule force spectroscopy: A facile technique for studying the interactions between biomolecules and materials interfaces

Wang

Qian

Sun

et al. 2020

Reviews in Analytical Chemistry

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The quantification of the interactions between biomolecules and materials interfaces is crucial for design and synthesis functional hybrid bionanomaterials for materials science, nanotechnology, biosensor, biomedicine, tissue engineering, and other applications. Atomic force spectroscopy (AFM)-based single-molecule force spectroscopy (SMFS) provides a direct way for measuring the binding and unbinding forces between various biomolecules (such as DNA, protein, peptide, antibody, antigen, and others) and different materials interfaces. Therefore, in this review, we summarize the advance of SMFS technique for studying the interactions between biomolecules and materials interfaces. To achieve this aim, firstly we introduce the methods for the functionalization of AFM tip and the preparation of functional materials interfaces, as well as typical operation modes of SMFS including dynamic force spectroscopy, force mapping, and force clamping. Then, typical cases of SMFS for studying the interactions of various biomolecules with materials interfaces are presented in detail. In addition, potential applications of the SMFS-based determination of the biomolecule-materials interactions for biosensors, DNA based mis-match, and calculation of binding free energies are also demonstrated and discussed. We believe this work will provide preliminary but important information for readers to understand the principles of SMFS experiments, and at the same time, inspire the utilization of SMFS technique for studying the intermolecular, intramolecular, and molecule-material interactions, which will be valuable to promote the reasonable design of biomolecule-based hybrid nanomaterials.

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“…Single-molecule force spectroscopy (SMFS), using an AFM, can directly measure the interactions between an amino acid or a peptide with a substrate. 19,20,21,22,23,24,25,26 Other methods such as phage display, 27,28 quartz crystal microbalance (QCM) 29 or surface plasmon resonance (SPR) 29,30,31,32,33 measure the interactions of peptides and proteins to inorganic surfaces in bulk. 34,35,36 This means that the results obtained by these methods relate to ensembles of molecules or aggregates.…”

Section: 161718mentioning

confidence: 99%

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy

Das

Duanias-Assaf

Reches

2017

JoVE

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The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

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Estimation of the free energy of adsorption of a polypeptide on amorphous SiO₂from molecular dynamics simulations and force spectroscopy experiments

Cited by 33 publications

References 77 publications

Delineating elastic properties of kinesin linker and their sensitivity to point mutations

Delineating elastic properties of kinesin linker and their sensitivity to point mutations

Single-molecule force spectroscopy: A facile technique for studying the interactions between biomolecules and materials interfaces

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy

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Estimation of the free energy of adsorption of a polypeptide on amorphous SiO2from molecular dynamics simulations and force spectroscopy experiments

Cited by 33 publications

References 77 publications

Delineating elastic properties of kinesin linker and their sensitivity to point mutations

Delineating elastic properties of kinesin linker and their sensitivity to point mutations

Single-molecule force spectroscopy: A facile technique for studying the interactions between biomolecules and materials interfaces

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy

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Estimation of the free energy of adsorption of a polypeptide on amorphous SiO₂from molecular dynamics simulations and force spectroscopy experiments