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1.
Carneiro FA Lapido-Loureiro PA Cordo SM Stauffer F Weissmüller G Bianconi ML Juliano MA Juliano L Bisch PM Da Poian AT Poian AT 《European biophysics journal : EBJ》2006,35(2):145-154
The entry of enveloped animal viruses into their host cells always depends on membrane fusion triggered by conformational
changes in viral envelope glycoproteins. Vesicular stomatitis virus (VSV) infection is mediated by virus spike glycoprotein
G, which induces membrane fusion between the viral envelope and the endosomal membrane at the acidic environment of this compartment.
In this work, we evaluated VSV interactions with membranes of different phospholipid compositions, at neutral and acidic pH,
using atomic force microscopy (AFM) operating in the force spectroscopy mode, isothermal calorimetry (ITC) and molecular dynamics
simulation. We found that the binding forces differed dramatically depending on the membrane phospholipid composition, revealing
a high specificity of G protein binding to membranes containing phosphatidylserine (PS). In a previous work, we showed that
the sequence corresponding amino acid 164 of VSV G protein was as efficient as the virus in catalyzing membrane fusion at
pH 6.0. Here, we used this sequence to explore VSV–PS interaction using ITC. We found that peptide binding to membranes was
exothermic, suggesting the participation of electrostatic interactions. Peptide–membrane interaction at pH 7.5 was shown to
be specific to PS and dependent on the presence of His residues in the fusion peptide. The application of the simplified continuum
Gouy–Chapman theory to our system predicted a pH of 5.0 at membrane surface, suggesting that the His residues should be protonated
when located close to the membrane. Molecular dynamics simulations suggested that the peptide interacts with the lipid bilayer
through its N-terminal residues, especially Val145 and His148.
Fabiana A.Carneiro and Pedro A. Lapido-Loureiro contributed equally to this work
An erratum to this article can be found at 相似文献
2.
Moldogazieva NT Shaitan KV Antonov MY Vinogradova IK Terentiev AA 《Biochemistry. Biokhimii?a》2011,76(12):1321-1336
Conformational and dynamic properties of proteins and peptides play an important role in their functioning. However, mechanisms
that underlie this influence have not been fully elucidated. In the present work we computationally constructed analogs of
heptapeptide AFP14–20 (LDSYQCT) — one of the biologically active sites of human α-fetoprotein (AFP) — to study their conformational and dynamic
properties using molecular dynamics simulation. Analogs were obtained by point substitutions of amino acid residues taking
into account differences in their physicochemical properties and also on the basis of analysis of amino acid substitutions
in the AFP14–20-like motifs revealed in different physiologically active proteins. It is shown that changes in conformational mobility of
amino acid residues of analogs are due to disruption or arising of intramolecular interactions that, in turn, determine existence
of steric restrictions during rotation around covalent bonds of the peptide backbone. Substitution of an amino acid by another
one with significant difference in physicochemical properties may not lead to remarkable changes in conformational and dynamic
properties of the peptide if intramolecular interactions remain unchanged. 相似文献
3.
The gap junction protein connexin43 (Cx43) binds to the second PDZ domain of Zonula occludens-1 (ZO-1) through its C-terminal tail, mediating the regulation of gap junction plaque size and dynamics. Biochemical study demonstrated that the very C-terminal 12 residues of Cx43 are necessary and sufficient for ZO-1 PDZ2 binding and phosphorylation at residues Ser (-9) and Ser (-10) of the peptide can disrupt the association. However, only a crystal structure of ZO-1 PDZ2 in complex with a shorter 9 aa peptide of connexin43 was solved experimentally. Here, the interactions between ZO-1 PDZ2 and the short, long and phosphorylated Cx43 peptides were studied using molecular dynamics (MD) simulations and free energy calculation. The short peptide bound to PDZ2 exhibits large structural variations, while the extension of three upstream residues stabilizes the peptide conformation and enhanced the interaction. Phosphorylation at Ser(-9) significantly weakens the binding and results in conformational flexibility of the peptide. Glu210 of ZO-1 PDZ2 was found to be a key regulatory point in Cx43 binding and phosphorylation induced dissociation. 相似文献
4.
5.
Dongxin Zhao Kui Lu Guangbin Liu Hanjing Zhu Li Ma Jianzhao Qi Libo Yuan 《Amino acids》2020,52(5):831-839
BRCA2 is an important tumor suppressor gene that plays a critical role in preserving the stability of cellular genetic information, participating in DNA repair by engaging in binding interactions with RAD51 proteins. However, the lack of structural data on BRCA2 and RAD51 makes the study of their interaction mechanism still a great challenge. We characterize the structure of the BRC8–RAD51 complex using ZDOCK protein docking software and identify the potential non-conserved active site of BRC8 via virtual alanine scanning, utilizing the obtained results to synthesize BRC8, its six analogous peptides (BRC8-1 to BRC8-6), and critical peptide fragment of RAD51 (RAD51(231–260)) by Fmoc solid-phase synthesis. The analogous peptides are found to exhibit a secondary structure significantly different from that of BRC8 by circular dichroism spectroscopy, which indicates that mutation sites determined by computer-aided simulation correspond to key amino acid residues substantially affecting polypeptide structure. On the other hand, the secondary structure of RAD51(231–260) was also considerably influenced by its interaction with BRC8 and analogs, e.g., the fraction of the α-helical structure in RAD51(231–260) increased to 23.6, 15.1, and 13.5% upon interaction with BRC8-1, BRC8-3, and BRC8-6, respectively. The results show that the properties of C-terminal amino acid residues significantly influence peptide–peptide interactions, in agreement with the results of virtual alanine scanning. Therefore, computer-aided simulation was confirmed to be a technique that is useful for narrowing down the range of sites responsible for interactions between peptides or proteins, and provides new inspirations for the design of peptides with strong interactions. 相似文献
6.
Human P450 protein CYP2C9 is one of the major drug-metabolizing isomers, contributing to the oxidation of 16% of the drugs
currently in clinical use. To examine the interaction mechanisms between CYP2C9 and proton pump inhibitions (PPIs), we used
molecular docking and molecular dynamics (MD) simulation methods to investigate the conformations and interactions around
the binding sites of PPIs/CYPP2C9. Results from molecular docking and MD simulations demonstrate that nine PPIs adopt two
different conformations (extended and U-bend structures) at the binding sites and position themselves far above the heme of
2C9. The presence of PPIs changes the secondary structures and residue flexibilities of 2C9. Interestingly, at the binding
sites of all PPI–CYP2C9 complexes except for Lan/CYP2C9, there are hydrogen-bonding networks made of PPIs, water molecules,
and some residues of 2C9. Moreover, there are strong hydrophobic interactions at all binding sites for PPIs/2C9, which indicate
that electrostatic interactions and hydrophobic interactions appear to be important for stabilizing the binding sites of most
PPIs/2C9. However, in the case of Lan/2C9, the hydrophobic interactions are more important than the electrostatic interactions
for stabilizing the binding site. In addition, an interesting conformational conversion from extended to U-bend structures
was observed for pantoprazole, which is attributed to an H-bond interaction in the binding pocket, an internal π–π stacking
interaction, and an internal electrostatic interaction of pantoprazole. 相似文献
7.
The quantum chemical and molecular dynamics studies have been performed to infer the structural changes of all-trans and all-cis
forms of cyclo[(1R,3S)-3-aminocyclohexanecarboxylicacid(γ-Acc)-α-Glycine(Gly)]3 hexapeptide. The backbone conformations of the above peptide have been analyzed using the valence and peptide deformation
angles applying B3LYP/6–311G** level of theory. The conformational preference of the backbone of all-trans and all-cis cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptides is found to depend on the puckering of cyclohexane rings. The non-uniform distribution of water inside the cavity
is observed, where sometimes water molecules formed a chain like conformation through hydrogen bond networks while traversing
the pore of all-cis cyclo[(1R,3S)-γ-Acc-Gly]3 peptide. Larger relaxation times of the order of a hundred to two hundred pico seconds for active site…water hydrogen bond
interactions were noticed. The hydrophobic nature of the cavity of all-trans cyclo[(1R,3S)-γ-Acc-Gly]3 due to the presence of cyclohexane moiety has been analyzed. Further this investigation emphasized on the non-transport of
molecules through the pore of all-trans cyclo[(1R,3S)-γ-Acc-Gly]3 peptide due to the obstruction produced by cyclohexane groups. 相似文献
8.
Tandon C De Lisle RC Boulatnikov I Naik PK 《Molecular and cellular biochemistry》2007,302(1-2):157-167
The C-terminal PDZ-binding motifs are required for polarized apical/basolateral localization of many membrane proteins. Ezrin–radixin–moesin
(ERM) proteins regulate the organization and function of specific cortical structures in polarized epithelial cells by connecting
filamentous (F)-actin to plasma membrane proteins through EBP50. Previous work showed that the membrane phosphoprotein apactin
(an 80-kDa type I membrane protein derived from pro-Muclin) is associated with the acinar cell apical actin cytoskeleton and
that this association is modulated by changes in the phosphorylation state of the apactin cytosolic tail. The carboxyl-terminal
amino acids of apactin (–STKL–COOH) are predicted to form a type I PDZ-binding domain, similar to that of CFTR (–DTRL–COOH).
Pairwise sequence comparison between NHERF/EBP50 and PDZK1/CAP70 PDZ domains reveals significant identity among the 83 amino-acid
residues (12–92) of EBP50 and CAP70 (241–323), which are involved in the interaction with the carboxyl-terminal peptides (STKL–COOH
and phosphomimetics) of apactin. Hence, the specificity and affinity of interactions are identical between them, which is
corroborated with the two hybrid results. Substitution of all the four-carboxyl-terminal amino acids in the wild type to Ala
reduces the interaction. Only the carbonyl oxygen and amide nitrogen of Ala are found to be involved in hydrogen bonding.
Further, truncation of the wild carboxyl-terminal peptide to RGQPP–COOH, showed very low affinity of interaction with PDZ1
domain. Only the atom Oε1 of Gln-2 hydrogen bonds with Nε2 of His72 of PDZ domain. Ser-3 amino acid in wild type apactin protein (STKL–COOH) is not involved in hydrogen bonding with
PDZ1 domain. However, substitution of Ser-3 to Asp-3 in PDTKL–COOH peptide increases the affinity of interaction of PDTKL–COOH
with PDZ1 domain. Thus, carboxyl-terminal Asp(D) -3, Thr(T) -2, Lys(K) -1 and Leu(L) 0 are involved in numerous interactions
with PDZ1 domains of NHERF/EBP50 and PDZK1/CAP70. 相似文献
9.
Takeshi Kobayakawa Shin-ichi Yamada Akio Mizuno Yuko Ohara-Nemoto Tomomi T. Baba Takayuki K. Nemoto 《The protein journal》2009,28(1):24-28
A single nucleotide polymorphism (SNP) that causes a missense mutation of highly conserved Gln488 to His of the α isoform
of the 90-kDa heat shock protein (Hsp90α) molecular chaperone is observed in Caucasians. The mutated Hsp90α severely reduced
the growth of yeast cells. To investigate this molecular mechanism, we examined the domain–domain interactions of human Hsp90α
by using bacterial 2-hybrid system. Hsp90α was expressed as a full-length form, N-terminal domain (residues 1–400), or middle
(residues 401–617) plus C-terminal (residues 618–732) domains (MC domain/amino acids 401–732). The Gln488His substitution
in MC domain did not affect the intra-molecular interaction with N-terminal domain, whereas the dimeric interaction-mediated
by the inter-molecular interaction between MC domains was decreased to 32%. Gln488Ala caused a similar change, whereas Gln488Thr,
which exceptionally occurs in mitochondrial Hsp90 paralog, fully maintained the dimeric interaction. Therefore, the SNP causing
Gln488His mutation could abrogate the Hsp90 function due to reduced dimerization. 相似文献
10.
A. A. Malygin E. I. Bondarenko V. A. Ivanisenko E. V. Protopopova G. G. Karpova V. B. Loktev 《Biochemistry. Biokhimii?a》2009,74(12):1328-1336
Polyclonal and monoclonal antibodies (MABs) to human laminin-binding protein (LBP) can efficiently block the penetration of
some alphaand flaviviruses into the cell. A panel of 13 types of MABs to human recombinant LBP was used for more detailed
study of the mechanism of this process. Competitive analysis has shown that MABs to LBP can be divided into six different
competition groups. MABs 4F6 and 8E4 classified under competition groups 3 and 4 can inhibit the replication of Venezuelan
equine encephalitis virus (VEEV), which is indicative of their interaction with the receptor domain of LBP providing for binding
with virions. According to enzyme immunoassay and immunoblotting data, polyclonal anti-idiotypic antibodies to MABs 4F6 and
8E4 modeling paratopes of the LBP receptor domain can specifically interact with VEEV E2 protein and tick-borne encephalitis
virus (TBEV) E protein. Mapping of binding sites of MABs 4F6 and 8E4 with LBP by constructing short deletion fragments of
the human LBP molecule has shown that MAB 8E4 interacts with the fragment of amino acid residues 187–210, and MAB 4F6 interacts
with the fragment of residues 263–278 of LBP protein, which is represented by two TEDWS peptides separated by four amino acid
residues. This suggested that the LBP receptor domain interacting with VEEV E2 and TBEV E viral proteins is located at the
C-terminal fragment of the LBP molecule. A model of the spatial structure of the LBP receptor domain distally limited by four
linear loops (two of which are represented by experimentally mapped regions of amino acid residues 187–210 and 263–278) as
well as the central β-folded region turning into the α-helical site including residues 200–216 of the LBP molecule and providing
for the interaction with the laminin-1 molecule has been proposed. 相似文献
11.
A. O. Shpakov E. A. Shpakova 《Biochemistry (Moscow) Supplemental Series B: Biomedical Chemistry》2011,5(3):246-252
In most serpentine type receptors the third intracellular loop (ICL-3) is responsible for the interaction with heterotrimeric
G proteins and for transduction of a hormonal signal to the enzymes, generators of the second messengers. It was found that
the peptides corresponding to ICL-3 influence functional activity of hormonal signaling systems in the absence of the hormone
and, consequently, may be considered as prototypes for the development of selective regulators of these systems. We have originally
synthesized peptides corresponding to the C-terminal regions 255–269 and 240–254 of ICL-3 of type 1 and 2 rat somatostatin
receptors (Som1R and Som2R). Micromolar concentrations of these peptides activated G
i
proteins and inhibited forskolin-stimulated activity of adenylyl cyclase (AC) in rat brain tissues. The peptide 255–269 of
Som1R is a selective antagonist of Som1R, and the peptide 240–254 of Som2R is an agonist of Som1R. The peptide 255–269 of Som1R decreased the regulatory effects of somatostatin and the selective Som1R agonist, CH-275, realized via the homologous receptor, while the peptide 240–254 of Som2R, on the contrary, increased the AC inhibitory effect of CH-275. Both peptides insignificantly influenced regulatory effects
of the Som2R agonist octreotide. Thus, the peptides studied by us are selective regulators of the somatostatin-sensitive AC system. Using
the peptides we have demonstrated that ICL-3 of both Som1R and Som2R includes the main molecular determinants that are responsible for activation of G
i
proteins and regulation of the AC system by somatostatin and its analogues. 相似文献
12.
Cátia Teixeira Florent Barbault Thierry Couesnon José R. B. Gomes Paula Gomes Fran?ois Maurel 《PloS one》2016,11(1)
HIV-1 gp41 facilitates the viral fusion through a conformational switch involving the association of three C-terminal helices along the conserved hydrophobic grooves of three N-terminal helices coiled-coil. The control of these structural rearrangements is thought to be central to HIV-1 entry and, therefore, different strategies of intervention are being developed. Herewith, we describe a procedure to simulate the folding of an HIV-1 gp41 simplified model. This procedure is based on the construction of plausible conformational pathways, which describe protein transition between non-fusogenic and fusogenic conformations. The calculation of the paths started with 100 molecular dynamics simulations of the non-fusogenic conformation, which were found to converge to different intermediate states. Those presenting defined criteria were selected for separate targeted molecular dynamics simulations, subjected to a force constant imposing a movement towards the gp41 fusogenic conformation. Despite significant diversity, a preferred sequence of events emerged when the simulations were analyzed in terms of the formation, breakage and evolution of the contacts. We pointed out 29 residues as the most relevant for the movement of gp41; also, 2696 possible interactions were reduced to only 48 major interactions, which reveals the efficiency of the method. The analysis of the evolution of the main interactions lead to the detection of four main behaviors for those contacts: stable, increasing, decreasing and repulsive interactions. Altogether, these results suggest a specific small cavity of the HIV-1 gp41 hydrophobic groove as the preferred target to small molecules. 相似文献
13.
Matthew S Najor Kenneth W Olsen Daniel J Graham Duarte Mota de Freitas 《Protein science : a publication of the Protein Society》2014,23(10):1392-1402
Giα1 is the inhibitory G-protein that, upon activation, reduces the activity of adenylyl cyclase. Comparison of the crystal structures of Giα1 bound to GDP•AMF or GTPγS with that of the inactive, GPD-bound protein indicates that a conformational change occurs in the activation step centered on three switch regions. The contribution of each tryptophan residue (W211 in the switch II region, W131 in the α-helical domain, and W258 in the GTPase domain) toward the intrinsic protein fluorescence was evaluated by using W211F, W131F, and W258F mutants. All three tryptophan residues contributed significantly toward the emission spectra regardless of the conformation. When activated by either GDP•AMF or GTPγS, the observed maximal-fluorescence scaled according to the solvent accessibilities of the tryptophan residues, calculated from molecular dynamics simulations. In the GDP•AMF and GTPγS, but not in the GDP, conformations, the residues W211 and R208 are in close proximity and form a π-cation interaction that results in a red shift in the emission spectra of WT, and W131F and W258F mutants, but a blue shift for the W211F mutant. The observed shifts did not show a relationship with the span of the W211-R208 bridge, but rather with changes in the total interaction energies. Trypsin digestion of the active conformations only occurred for the W211F mutant indicating that the electrostatic π-cation interaction blocks access to R208, which was consistent with the molecular dynamics simulations. We conclude that solvent accessibility and interaction energies account for the fluorescence features of Giα1. 相似文献
14.
The main component of senile plaques found in AD brain is amyloid β-peptide (Aβ), and the neurotoxicity and aggregation of
Aβ are associated with the formation of β-sheet structure. Experimentally, beta sheet breaker (BSB) peptide fragment Leu-Pro-Phe-Phe-Asp
(LPFFD) can combine with Aβ, which can inhibit the aggregation of Aβ. In order to explore why LPFFD can inhibit the formation
of β-sheet conformation of Aβ at atomic level, first, molecular docking is performed to obtain the binding sites of LPFFD
on the Aβ(1–42) (LPFFD/Aβ(1–42)), which is taken as the initial conformation for MD simulations. Then, MD simulations on LPFFD/Aβ(1–42)
in water are carried out. The results demonstrate that LPFFD can inhibit the conformational transition from α-helix to β-sheet
structure for the C-terminus of Aβ(1–42), which may be attributed to the hydrophobicity decreasing of C-terminus residues
of Aβ(1–42) and formation probability decreasing of the salt bridge Asp23-Lys28 in the presence of LPFFD. 相似文献
15.
Retinol binding protein (RBP) and an engineered lipocalin, DigA16, have been studied using molecular dynamics simulations.
Special emphasis has been placed on explaining the ligand–receptor interaction in RBP–retinol and DigA16–digoxigenin complexes,
and steered molecular dynamics simulations of 10–20 ns have been carried out for the ligand expulsion process. Digoxigenin
is bound deep inside the cavity of DigA16 and forms several stable hydrogen bonds in addition to the hydrophobic van der Waals
interaction with the aromatic side-chains. Four crystalline water molecules inside the ligand-binding cavity remain trapped
during the simulations. The strongly hydrophobic receptor site of RBP differs considerably from DigA16, and the main source
of ligand attraction comes from the phenyl side-chains. The hydrogen bonds between digoxigenin and DigA16 cause the rupture
forces on ligand removal in DigA16 and RBP to differ. The mutated DigA16 residues contribute approximately one-half of the
digoxigenin interaction energy with DigA16 and, of these, the energetically most important are residues His35, Arg58, Ser87,
Tyr88, and Phe114. Potential “sensor loops” were found for both receptors. These are the outlier loops between residues 114–121
and 63–67 for DigA16 and RBP, respectively, and they are located near the entrance of the ligand-binding cavity. Especially,
the residues Glu119 (DigA16) and Leu64 (RBP) are critical for sensing. The ligand binding energies have been estimated based
on the linear response approximation of binding affinity by using a previous parametrization for retinoids and RBP. 相似文献
16.
Stavrakoudis A 《Cell biochemistry and biophysics》2011,60(3):283-295
One key step in the immune response against infected or tumor cells is the recognition of the T-cell receptor (TCR) by class
I major histocompatibility complexes. The complex between the HLA-B8 molecule and the immunodominant peptide with sequence
FLRGRAYGL, derived from the Epstein-Barr virus, with the LC13 TCR has been determined by X-ray diffraction. The complex has been used as a starting point in a molecular
dynamics study in order to investigate the dynamics of the complex association and to explore the specific interactions of
the complex formation. The analyzed structures provided evidence that the peptide adopts an open type β-turn conformation
close to C-terminal part, which dominates peptide/TCR interactions. Conformational energy landscape analysis indicated the
presence of two conformational clusters in the peptide’s structure, underlying the backbone flexibility of the peptide despite
being surrounded by two receptors. The peptide/MHC/TCR interface was found to hold significant number of solvent molecules,
more specifically the peptide has been found to have approximately seventeen hydrogen bonds with water molecules. The molecular
dynamics simulation indicated the disruption of some MHC/TCR contacts, mainly with the CDR1α loop. However, several other
interactions emerged that resulted in a stable association during the 20 ns trajectory, as revealed by the buried surface
area analysis. 相似文献
17.
Anna Maria Dursi Stefania Albrizio Giovanni Greco Sonia Mazzeo Maria R Mazzoni Etrore Novellino Paolo Rovero 《Journal of peptide science》2002,8(8):476-488
The C-terminal domain of the heterotrimeric G protein a-subunits plays a key role in selective activation of G proteins by their cognate receptors. Several C-terminal fragments of Galpha(s) (from 11 to 21 residues) were recently synthesized. The ability of these peptides to stimulate agonist binding was found to be related to their size. Galpha(s)(380-394) is a 15-mer peptide of intermediate length among those synthesized and tested that displays a biological activity surprisingly weak compared with that of the corresponding 21-mer peptide, shown to be the most active. In the present investigation, Galpha(s)(380-394) was subjected to a conformational NMR analysis in a fluorinated isotropic environment. An NMR structure, calculated on the basis of the data derived from conventional 1D and 2D homonuclear experiments, shows that the C-terminal residues of Galpha(s)(380-394) are involved in a helical arrangement whose length is comparable to that of the most active 21 -mer peptide. A comparative structural refinement of the NMR structures of Galpha(s)(380-394) and Galpha(s)(374-394)C379A was performed using molecular dynamics calculations. The results give structural elements to interpret the role played by both the backbone conformation and the side chain arrangement in determining the activity of the G protein C-terminal fragments. The orientation of the side chains allows the peptides to assume contacts crucial for the G protein/receptor interaction. In the 15-mer peptide the lack as well as the disorder of some N-terminal residues could explain the low biological activity observed. 相似文献
18.
Shine Ayyappan Pooja S. Dharan Arya Krishnan Renjith R. Marira Mahil Lambert Tapas K. Manna Vinesh Vijayan 《Biophysical journal》2021,120(10):2019-2029
SxIP is a microtubule tip localizing signal found in many +TIP proteins that bind to the hydrophobic cavity of the C-terminal domain of end binding protein 1 (EB1) and then positively regulate the microtubule plus-end tracking of EBs. However, the exact mechanism of microtubule activation of EBs in the presence of SxIP signaling motif is not known. Here, we studied the effect of SxIP peptide on the native conformation of EB1 in solution. Using various NMR experiments, we found that SxIP peptide promoted the dissociation of natively formed EB1 dimer. We also discovered that I224A mutation of EB1 resulted in an unfolded C-terminal domain, which upon binding with the SxIP motif folded to its native structure. Molecular dynamics simulations also confirmed the relative structural stability of EB1 monomer in the SxIP bound state. Residual dipolar couplings and heteronuclear NOE analysis suggested that the binding of SxIP peptide at the C-terminal domain of EB1 decreased the dynamics and conformational flexibility of the N-terminal domain involved in EB1-microtubule interaction. The SxIP-induced disruption of the dimeric interactions in EB1, coupled with the reduction in conformational flexibility of the N-terminal domain of EB1, might facilitate the microtubule association of EB1. 相似文献
19.
Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2‐3)Gal: a study by in silico mutations and molecular dynamics simulations
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Ponnusamy Parasuraman Veeramani Murugan Jeyasigamani F. A. Selvin M. Michael Gromiha Kazuhiko Fukui Kasinadar Veluraja 《Journal of molecular recognition : JMR》2014,27(8):482-492
Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at the active site of WGA to enhance the binding specificity towards sialylglycans, and molecular dynamics simulations of 20 ns are carried out for wild type and mutated WGAs (WGA1, WGA2, and WGA3) in complex with sialylgalactose to examine the change in binding specificity. MD simulations reveal the change in binding specificity of wild type and mutated WGAs towards sialylgalactose and bound conformational flexibility of sialylgalactose. The mutated polar amino acid residues Asn114 (S114N), Lys118 (G118K), and Arg118 (G118R) make direct and water mediated hydrogen bonds and hydrophobic interactions with sialylgalactose. An analysis of possible hydrogen bonds, hydrophobic interactions, total pair wise interaction energy between active site residues and sialylgalactose and MM‐PBSA free energy calculation reveals the plausible binding modes and the role of water in stabilizing different binding modes. An interesting observation is that the binding specificity of mutated WGAs (cyborg lectin) towards sialylgalactose is found to be higher in double point mutation (WGA3). One of the substituted residues Arg118 plays a crucial role in sugar binding. Based on the interactions and energy calculations, it is concluded that the order of binding specificity of WGAs towards sialylgalactose is WGA3 > WGA1 > WGA2 > WGA. On comparing with the wild type, double point mutated WGA (WGA3) exhibits increased specificity towards sialylgalactose, and thus, it can be effectively used in targeted drug delivery and as biological cell marker in cancer therapeutics. Copyright © 2014 John Wiley & Sons, Ltd. 相似文献
20.
《Biochimica et Biophysica Acta - Proteins and Proteomics》2022,1870(3):140756
Nicking endonuclease Nt.BspD6I (Nt.BspD6I) is the large subunit of the heterodimeric restriction endonuclease R.BspD6I. It recognizes the short specific DNA sequence 5´′- GAGTC and cleaves only the top strand in dsDNA at a distance of four nucleotides downstream the recognition site toward the 3´′-terminus. A mechanism of interaction of this protein with DNA is still unknown. Here we report the crystal structure of Cysteine-free Nt.BspD6I, with four cysteine residues (11, 160, 508, 578) substituted by serine, which was determined with a resolution of 1.93 Å. A comparative structural analysis showed that the substitution of cysteine residues induced marked conformational changes in the N-terminal recognition and the C-terminal cleavage domains. As a result of this changes were formed three new hydrogen bonds and the electrostatic field in these regions changed compared with wild type Nt.BspD6I. The substitution of cysteine residues did not alter the nicking function of Cysteine-free Nt.BspD6I but caused change in the activity of Cysteine-free heterodimeric restriction endonuclease R.BspD6I due to a change in the interaction between its large and small subunits. The results obtained contribute to the identification of factors influencing the interactions of subunits in the heterodimeric restriction enzyme R.BspD6I. 相似文献