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1.
Mateusz Chwastyk Albert Galera–Prat Mateusz Sikora Àngel Gómez‐Sicilia Mariano Carrión‐Vázquez Marek Cieplak 《Proteins》2014,82(5):717-726
We provide theoretical tests of a novel experimental technique to determine mechanostability of proteins based on stretching a mechanically protected protein by single‐molecule force spectroscopy. This technique involves stretching a homogeneous or heterogeneous chain of reference proteins (single‐molecule markers) in which one of them acts as host to the guest protein under study. The guest protein is grafted into the host through genetic engineering. It is expected that unraveling of the host precedes the unraveling of the guest removing ambiguities in the reading of the force‐extension patterns of the guest protein. We study examples of such systems within a coarse‐grained structure‐based model. We consider systems with various ratios of mechanostability for the host and guest molecules and compare them to experimental results involving cohesin I as the guest molecule. For a comparison, we also study the force‐displacement patterns in proteins that are linked in a serial fashion. We find that the mechanostability of the guest is similar to that of the isolated or serially linked protein. We also demonstrate that the ideal configuration of this strategy would be one in which the host is much more mechanostable than the single‐molecule markers. We finally show that it is troublesome to use the highly stable cystine knot proteins as a host to graft a guest in stretching studies because this would involve a cleaving procedure. Proteins 2014; 82:717–726. © 2014 Wiley Periodicals, Inc. 相似文献
2.
《Structure (London, England : 1993)》2022,30(9):1354-1365.e5
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3.
Theoretical exploration of fundamental biological processes involving the forced unraveling of multimeric proteins, the sliding motion in protein fibers and the mechanical deformation of biomolecular assemblies under physiological force loads is challenging even for distributed computing systems. Using a Cα‐based coarse‐grained self organized polymer (SOP) model, we implemented the Langevin simulations of proteins on graphics processing units (SOP‐GPU program). We assessed the computational performance of an end‐to‐end application of the program, where all the steps of the algorithm are running on a GPU, by profiling the simulation time and memory usage for a number of test systems. The ～90‐fold computational speedup on a GPU, compared with an optimized central processing unit program, enabled us to follow the dynamics in the centisecond timescale, and to obtain the force‐extension profiles using experimental pulling speeds (vf = 1–10 μm/s) employed in atomic force microscopy and in optical tweezers‐based dynamic force spectroscopy. We found that the mechanical molecular response critically depends on the conditions of force application and that the kinetics and pathways for unfolding change drastically even upon a modest 10‐fold increase in vf. This implies that, to resolve accurately the free energy landscape and to relate the results of single‐molecule experiments in vitro and in silico, molecular simulations should be carried out under the experimentally relevant force loads. This can be accomplished in reasonable wall‐clock time for biomolecules of size as large as 105 residues using the SOP‐GPU package. Proteins 2010; © 2010 Wiley‐Liss, Inc. 相似文献
4.
Shulin Zhuang Apichart Linhananta Hongbin Li 《Protein science : a publication of the Protein Society》2010,19(11):2231-2239
Tenascin‐X (TNX) is an extracellular matrix (ECM) protein and interacts with a wide variety of molecules in the ECM as well as on the membrane. Deficiency of TNX causes a recessive form of Ehlers–Danlos syndrome (EDS) characterized by hyperelastic and fragile skin, easy bruising, and hypermobile joints. Three point mutations in TNX gene were found to be associated with hypermobility type EDS and one of such mutations is the V1195M mutation at the 7th fibronectin Type III domain (TNXfn7). To help elucidate the underlying molecular mechanism connecting this mutation to EDS, here we combined homology modeling, chemical denaturation, single molecule atomic force microscopy, and molecular dynamics (MD) simulation techniques to investigate the phenotypic effects of V1195M on TNXfn7. We found that the V1195M mutation does not alter the three‐dimensional structure of TNXfn7 and had only mild destabilization effects on the thermodynamic and mechanical stability of TNXfn7. However, MD simulations revealed that the mutation V1195M significantly alters the flexibility of the C′E loop of TNXfn7. As loops play important roles in protein–protein and protein–ligand interactions, we hypothesize that the decreased loop flexibility by V1195M mutation may affect the binding of TNX to ECM molecules and thus adversely affect collagen deposition and fibrillogenesis. Our results may provide new insights in understanding the molecular basis for the pathogenesis of V1195M‐resulted EDS. 相似文献
5.
Molecular imprinting is an established method for the creation of artificial recognition sites in synthetic materials through polymerization and cross-linking in the presence of template molecules. Removal of the templates leaves cavities that are complementary to the template molecules in size, shape, and functionality. In recent years, various theoretical and computational models have been developed as tools to aid in the design of molecularly imprinted polymers (MIPs) or to provide insight into the features that determine MIP performance. These studies can be grouped into two general approaches-screening for possible functional monomers for particular templates and macromolecular models focusing on the structural characterization of the imprinted material. In this review, we pay special attention to coarse-grained models that characterize the functional heterogeneity in imprinted pores, but also cover recent advances in atomistic and first principle studies. We offer a critical assessment of the potential impact of the various models towards improving the state-of-the-art of molecular imprinting. 相似文献
6.
Alzheimer's, Parkinson's, and Creutzfeldt-Jakob's neurodegenerative diseases are all linked with the assembly of normally soluble proteins into amyloid fibrils. Because of experimental limitations, structural characterization of the soluble oligomers, which form early in the process of fibrillogenesis and are cytotoxic, remains to be determined. In this article, we study the aggregation paths of seven chains of the shortest amyloid-forming peptide, using an activitated method and a reduced atomic representation. Our simulations show that disordered KFFE monomers ultimately form three distinct topologies of similar energy: amorphous oligomers, incomplete rings with beta-barrel character, and cross-beta-sheet structures with the meridional but not the equatorial X-ray fiber reflections. The simulations also shed light on the pathways from misfolded aggregates to fibrillar-like structures. They also underline the multiplicity of building blocks that can lead to the formation of the critical nucleus from which rapid growth of the fibril occurs. 相似文献
7.
Wenxue Liang Haitao Yang Xiaoyu Xue Qiuhua Huang Mark Bartlam Saijuan Chen 《Acta Crystallographica. Section F, Structural Biology Communications》2006,62(6):556-558
Palladin is a member of the recently discovered palladin/myotilin/myopalladin family, the members of which associate with α‐actinin. Palladin may play important roles in actin stress‐fibre formation, cell adhesion and migration. The immunoglobulin‐like domain 3 of human palladin has been overexpressed in Escherichia coli and crystallized suitable for X‐ray crystallographic study. Crystals have been obtained using the vapour‐diffusion method and belong to space group P21. X‐ray diffraction data were collected in‐house to 1.8 Å resolution from a single crystal. The unit‐cell parameters are a = 40.9, b = 33.3, c = 34.8 Å, β = 90.3°. One molecule was predicted to be present in the asymmetric unit. 相似文献
8.
Amyloid protein aggregation characterizes many neurodegenerative disorders, including Alzheimer's, Parkinson's, and Creutzfeldt‐Jakob disease. Evidence suggests that amyloid aggregates may share similar aggregation pathways, implying simulation of full‐length amyloid proteins is not necessary for understanding amyloid formation. In this study, we simulate GNNQQNY, the N‐terminal prion‐determining domain of the yeast protein Sup35 to investigate the thermodynamics of structural transitions during aggregation. Utilizing a coarse‐grained model permits equilibration on relevant time scales. Replica‐exchange molecular dynamics is used to gather simulation statistics at multiple temperatures and clear energy traps that would aversely impact results. Investigating the association of 3‐, 6‐, and 12‐chain GNNQQNY systems by calculating thermodynamic quantities and orientational order parameters, we determine the aggregation pathway by studying aggregation states of GNNQQNY. We find that the aggregation of the hydrophilic GNNQQNY sequence is mainly driven by H‐bond formation, leading to the formation of β‐sheets from the very beginning of the assembly process. Condensation (aggregation) and ordering take place simultaneously, which is underpinned by the occurrence of a single heat capacity peak. Proteins 2013; 81:1141–1155. © 2013 Wiley Periodicals, Inc. 相似文献
9.
The characterization of elastic properties of biopolymers is crucial to understand many molecular reactions determined by conformational bending fluctuations of the polymer. Direct measurement of such elastic properties using single‐molecule methods is usually hindered by the intrinsic tendency of such biopolymers to form high‐order molecular structures. For example, single‐stranded deoxyribonucleic acids (ssDNA) tend to form secondary structures such as local double helices that prevent the direct measurement of the ideal elastic response of the ssDNA. In this work, we show how to extract the ideal elastic response in the entropic regime of short ssDNA molecules by mechanically pulling two‐state DNA hairpins of different contour lengths. This is achieved by measuring the force dependence of the molecular extension and stiffness on mechanically folding and unfolding the DNA hairpin. Both quantities are fit to the worm‐like chain elastic model giving values for the persistence length and the interphosphate distance. This method can be used to unravel the elastic properties of short ssDNA and RNA sequences and, more generally, any biopolymer that can exhibit a cooperative two‐state transition between mechanically folded and unfolded states (such as proteins). © 2014 Wiley Periodicals, Inc. Biopolymers 101: 1193–1199, 2014. 相似文献
10.
The prion-forming C-terminal domain of the fungal prion HET-s forms infectious amyloid fibrils at physiological pH. The conformational switch from the nonprion soluble form to the prion fibrillar form is believed to have a functional role, as HET-s in its prion form participates in a recognition process of different fungal strains. On the basis of the knowledge of the high-resolution structure of the prion forming domain HET-s(218-289) in its fibrillar form, we here present a numerical simulation of the fibril growth process, which emphasizes the role of the topological properties of the fibrillar structure. An accurate thermodynamic analysis of the way an intervening HET-s chain is recruited to the tip of the growing fibril suggests that elongation proceeds through a dock and lock mechanism. First, the chain docks onto the fibril by forming the longest β-strands. Then, the re-arrangement in the fibrillar form of all the rest of the molecule takes place. Interestingly, we also predict that one side of the HET-s fibril is more suitable for sustaining its growth with respect to the other. The resulting strong polarity of fibril growth is a consequence of the complex topology of HET-s fibrillar structure, as the central loop of the intervening chain plays a crucially different role in favoring or not the attachment of the C-terminus tail to the fibril, depending on the growth side. 相似文献
11.
Joost te Riet Inge Reinieren‐Beeren Carl G. Figdor Alessandra Cambi 《Journal of molecular recognition : JMR》2015,28(11):687-698
The fungus Candida albicans is the most common cause of mycotic infections in immunocompromised hosts. Little is known about the initial interactions between Candida and immune cell receptors, such as the C‐type lectin dendritic cell‐specific intracellular cell adhesion molecule‐3 (ICAM‐3)‐grabbing non‐integrin (DC‐SIGN), because a detailed characterization at the structural level is lacking. DC‐SIGN recognizes specific Candida‐associated molecular patterns, that is, mannan structures present in the cell wall of Candida. The molecular recognition mechanism is however poorly understood. We postulated that small differences in mannan‐branching may result in considerable differences in the binding affinity. Here, we exploit atomic force microscope‐based dynamic force spectroscopy with single Candida cells to gain better insight in the carbohydrate recognition capacity of DC‐SIGN. We demonstrate that slight differences in the N‐mannan structure of Candida, that is, the absence or presence of a phosphomannan side chain, results in differences in the recognition by DC‐SIGN as follows: (i) it contributes to the compliance of the outer cell wall of Candida, and (ii) its presence results in a higher binding energy of 1.6 kBT. The single‐bond affinity of tetrameric DC‐SIGN for wild‐type C. albicans is ~10.7 kBT and a dissociation constant kD of 23 μM, which is relatively strong compared with other carbohydrate–protein interactions described in the literature. In conclusion, this study shows that DC‐SIGN specifically recognizes mannan patterns on C. albicans with high affinity. Knowledge on the binding pocket of DC‐SIGN and its pathogenic ligands will lead to a better understanding of how fungal‐associated carbohydrate structures are recognized by receptors of the immune system and can ultimately contribute to the development of new anti‐fungal drugs. Copyright © 2015 John Wiley & Sons, Ltd. 相似文献
12.
Protein loops are essential structural elements that influence not only function but also protein stability and folding rates. It was recently reported that shortening a loop in the AcP protein may increase its native state conformational entropy. This effect on the entropy of the folded state can be much larger than the lower entropic penalty of ordering a shorter loop upon folding, and can therefore result in a more pronounced stabilization than predicted by polymer model for loop closure entropy. In this study, which aims at generalizing the effect of loop length shortening on native state dynamics, we use all‐atom molecular dynamics simulations to study how gradual shortening a very long or solvent‐exposed loop region in four different proteins can affect their stability. For two proteins, AcP and Ubc7, we show an increase in native state entropy in addition to the known effect of the loop length on the unfolded state entropy. However, for two permutants of SH3 domain, shortening a loop results only with the expected change in the entropy of the unfolded state, which nicely reproduces the observed experimental stabilization. Here, we show that an increase in the native state entropy following loop shortening is not unique to the AcP protein, yet nor is it a general rule that applies to all proteins following the truncation of any loop. This modification of the loop length on the folded state and on the unfolded state may result with a greater effect on protein stability. Proteins 2015; 83:2137–2146. © 2015 Wiley Periodicals, Inc. 相似文献
13.
Aggregation of the Abeta1-40/Abeta1-42 peptides is a key factor in Alzheimer's disease. Though the inhibitory effect of N-methylated Abeta16-22 (mAbeta16-22) peptides is well characterized in vitro, there is little information on how they disassemble full-length Abeta fibrils or block fibril formation. Here, we report coarse-grained implicit solvent molecular dynamics (MD) and replica exchange molecular dynamics (REMD) simulations on Abeta16-22 and mAbeta16-22 monomers, and then a preformed six-chain Abeta16-22 bilayer with either four copies of Abeta16-22 or four copies of mAbeta16-22. Our simulations show that the effect of N-methylation on mAbeta16-22 monomer is to reduce the density of compact forms. While 100 ns MD trajectories do not reveal any significant differences between the two ten-chain systems, the REMD simulations totaling 1 micros help understand the first steps of Abeta16-22 protofibril disassembly by N-methylated inhibitors. Notably, we find that mAbeta16-22 preferentially interacts with Abeta16-22 by blocking both beta-sheet extension and lateral association of layers, but also by intercalation of the inhibitors allowing sequestration of Abeta16-22 peptides. This third binding mode is particularly appealing for blocking Abeta fibrillogenesis. 相似文献
14.
15.
Xin Fu Yan Xu Chenyu Wu Vincent T. Moy X. Frank Zhang 《Journal of molecular recognition : JMR》2015,28(6):385-392
The dynamic interactions between leukocyte integrin receptors and ligands in the vascular endothelium, extracellular matrix, or invading pathogens result in leukocyte adhesion, extravasation, and phagocytosis. This work examined the mechanical strength of the connection between iC3b, a complement component that stimulates phagocytosis, and the ligand‐binding domain, the I‐domain, of integrin αMβ2. Single‐molecule force measurements of αM I‐domain–iC3b complexes were conducted by atomic force microscope. Strikingly, depending on loading rates, immobilization of the I‐domain via its C‐terminus resulted in a 1.3‐fold to 1.5‐fold increase in unbinding force compared with I‐domains immobilized via the N‐terminus. The force spectra (unbinding force versus loading rate) of the I‐domain–iC3b complexes revealed that the enhanced mechanical strength is due to a 2.4‐fold increase in the lifetime of the I‐domain–iC3b bond. Given the structural and functional similarity of all integrin I‐domains, our result supports the existing allosteric regulatory model by which the ligand binding strength of integrin can be increased rapidly when a force is allowed to stretch the C‐terminus of the I‐domain. This type of mechanism may account for the rapid ligand affinity adjustment during leukocyte migration. Copyright © 2015 John Wiley & Sons, Ltd. 相似文献
16.
The 2013 Nobel Prize in Chemistry has convinced the world that how important the role that computational sciences play in chemical and materials sciences. In this review, computational methods and rational molecule design, including quantum mechanics and molecular mechanics methods, have been applied to study electronic structures and the interactions in a number of important applications at molecular level. The applications which include bioactive compounds, drug candidates and photoactive molecules at Swinburne University in the past several years are discussed. The research is in close collaboration with world class experimental groups from spectroscopy, organic and medicinal synthesis laboratories and most recently to γ-ray spectroscopy as well as other theory groups in the world. Ionisation spectra of biomolecules and bioactive compounds including amino acids, DNA bases, cyclic dipeptides, drug candidates, complexes and photoactive molecules are discussed. Most recent projects such as infrared spectral studies of ferrocene, rational design of organic dyes in solar cell applications, and recent development in γ-ray spectra of positron annihilation in molecules are highlighted. 相似文献
17.
Hideaki Tamai Naoko Okutsu Yuki Tokuyama Eisuke Shimizu Satoshi Miyagi Sergiy Shulga 《Molecular simulation》2016,42(2):122-130
The dependence of geometric structure and thermal stability of liposomes on their component phospholipid molecules and distribution of molecules in the inner and the outer layers of the liposome is investigated by conducting molecular simulations in explicit water for the eight types of liposomes constructed from different phospholipids. Using molecular mechanics structure-relaxation based on the coarse grained (CG) model, stable structures of the solvated liposomes are obtained. In addition, the molecular dynamics (MD) simulations based on the CG model are carried out at 310 and 360 K for elucidating the change in structure of the solvated liposomes. The MD simulations reveal that liposomes having the same number of lipids (SNL) in both the inner and the outer layers keep their spherical structures even at 360 K. In particular, the SNLs composed of palmitoyloleoyl-phosphatidyl-ethanolamine1 or dimyristoylglycero-phosphatidyl-choline lipid exhibit a compact spherical shape. In contrast, liposomes having the same density of lipids in the inner and the outer layers cannot keep their spherical shapes at 360 K. The obtained results contribute toward developing novel liposomes with enhanced thermal stability. 相似文献
18.
Coupled binding and folding is frequently involved in specific recognition of so-called intrinsically disordered proteins (IDPs), a newly recognized class of proteins that rely on a lack of stable tertiary fold for function. Here, we exploit topology-based Gō-like modeling as an effective tool for the mechanism of IDP recognition within the theoretical framework of minimally frustrated energy landscape. Importantly, substantial differences exist between IDPs and globular proteins in both amino acid sequence and binding interface characteristics. We demonstrate that established Gō-like models designed for folded proteins tend to over-estimate the level of residual structures in unbound IDPs, whereas under-estimating the strength of intermolecular interactions. Such systematic biases have important consequences in the predicted mechanism of interaction. A strategy is proposed to recalibrate topology-derived models to balance intrinsic folding propensities and intermolecular interactions, based on experimental knowledge of the overall residual structure level and binding affinity. Applied to pKID/KIX, the calibrated Gō-like model predicts a dominant multistep sequential pathway for binding-induced folding of pKID that is initiated by KIX binding via the C-terminus in disordered conformations, followed by binding and folding of the rest of C-terminal helix and finally the N-terminal helix. This novel mechanism is consistent with key observations derived from a recent NMR titration and relaxation dispersion study and provides a molecular-level interpretation of kinetic rates derived from dispersion curve analysis. These case studies provide important insight into the applicability and potential pitfalls of topology-based modeling for studying IDP folding and interaction in general. 相似文献
19.
The goal of this work is to understand how the sequence of a protein affects the likelihood that it will form an amyloid fibril and the kinetics along the fibrillization pathway. The focus is on very short fragments of amyloid proteins since these play a role in the fibrillization of the parent protein and can form fibrils themselves. Discontinuous molecular dynamics simulations using the PRIME20 force field were performed of the aggregation of 48‐peptide systems containing SNQNNF ( PrP (170–175 )), SSTSAA (RNaseA(15–20)), MVGGVV (Aβ(35–40)), GGVVIA (Aβ(37–42)), and MVGGVVIA (Aβ(35–42)). In our simulations SNQQNF, SSTTSAA, and MVGGVV form large numbers of fibrillar structures spontaneously (as in experiment). GGVVIA forms β‐sheets that do not stack into fibrils (unlike experiment). The combination sequence MVGGVVIA forms less fibrils than MVGGVV, hindered by the presence of the hydrophobic residues at the C‐terminal. Analysis of the simulation kinetics and energetics reveals why MVGGVV forms fibrils and GGVVIA does not, and why adding I and A to MVGGVVIA reduces fibrillization and enhances amorphous aggregation into oligomeric structures. The latter helps explain why Aβ(1–42) assembles into more complex oligomers than Aβ(1–40), a consequence of which is that it is more strongly associated with Alzheimer's disease. Proteins 2014; 82:1469–1483. © 2014 Wiley Periodicals, Inc. 相似文献
20.
The conformational properties of unbound multi‐Cys2His2 (mC2H2) zinc finger proteins, in which zinc finger domains are connected by flexible linkers, are studied by a multiscale approach. Three methods on different length scales are utilized. First, atomic detail molecular dynamics simulations of one zinc finger and its adjacent flexible linker confirmed that the zinc finger is more rigid than the flexible linker. Second, the end‐to‐end distance distributions of mC2H2 zinc finger proteins are computed using an efficient atomistic pivoting algorithm, which only takes excluded volume interactions into consideration. The end‐to‐end distance distribution gradually changes its profile, from left‐tailed to right‐tailed, as the number of zinc fingers increases. This is explained by using a worm‐like chain model. For proteins of a few zinc fingers, an effective bending constraint favors an extended conformation. Only for proteins containing more than nine zinc fingers, is a somewhat compacted conformation preferred. Third, a mesoscale model is modified to study both the local and the global conformational properties of multi‐C2H2 zinc finger proteins. Simulations of the CCCTC‐binding factor (CTCF), an important mC2H2 zinc finger protein for genome spatial organization, are presented. Proteins 2015; 83:1604–1615. © 2015 Wiley Periodicals, Inc. 相似文献