Structural Dynamics of α-Actinin-Vinculin Interactions

ABSTRACT α-Actinin and vinculin orchestrate reorganization of the actin cytoskeleton following the formation of adhesion junctions. α-Actinin interacts with vinculin through the binding of an α-helix (αVBS) present within the R4 spectrin repeat of its central rod domain to vinculin's N-terminal seven-helical bundle domain (Vh1). The Vh1:αVBS structure suggests that αVBS first unravels from its buried location in the triple-helical R4 repeat to allow it to bind to vinculin. αVBS binding then induces novel conformational changes in the N-terminal helical bundle of Vh1, which disrupt its intramolecular association with vinculin's tail domain and which differ from the alterations in Vh1 provoked by the binding of talin. Surprisingly, αVBS binds to Vh1 in an inverted orientation compared to the binding of talin's VBSs to vinculin. Importantly, the binding of αVBS and talin's VBSs to vinculin's Vh1 domain appear to also trigger distinct conformational changes in full-length vinculin, opening up distant regions that are buried in the inactive molecule. The data suggest a model where vinculin's Vh1 domain acts as a molecular switch that undergoes distinct structural changes provoked by talin and α-actinin binding in focal adhesions versus adherens junctions, respectively.

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Cryo-EM Structures of HIV-1 trimer bound to CD4-mimetics M48U1 and BNM-III-170 adopt a CD4-bound open conformation

10.1101/2020.08.21.261974 ◽

2020 ◽

Author(s):

Claudia A. Jette ◽

Christopher O. Barnes ◽

Sharon M. Kirk ◽

Bruno Melillo ◽

Amos B. Smith ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Membrane Fusion ◽

Conformational Changes ◽

Structural Changes ◽

Target Cells ◽

Helical Bundle ◽

Open Conformation ◽

Immunodeficiency Virus ◽

Hiv 1 ◽

Human Immunodeficiency Virus 1

AbstractHuman Immunodeficiency Virus-1 (HIV-1), the causative agent of AIDS, impacts millions of people. Entry into target cells is mediated by the HIV-1 envelope (Env) glycoprotein interacting with host receptor CD4, which triggers conformational changes allowing binding to a coreceptor and subsequent membrane fusion. Small molecule or peptide CD4-mimetic drugs mimic CD4’s Phe43 interaction with Env by inserting into the conserved Phe43 pocket on Env subunit gp120. Here, we present single-particle cryo-EM structures of CD4-mimetics BNM-III-170 and M48U1 bound to a BG505 native-like Env trimer plus the CD4-induced antibody 17b at 3.7Å and 3.9Å resolution, respectively. CD4-mimetic-bound BG505 exhibits canonical CD4-induced conformational changes including trimer opening, formation of the 4-stranded gp120 bridging sheet, displacement of the V1V2 loop, and formation of a compact and elongated gp41 HR1C helical bundle. We conclude that CD4-induced structural changes on both gp120 and gp41 Env subunits are induced by binding to the gp120 Phe43 pocket.

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Protein Conformational Changes in Breast Cancer Sera Using Infrared Spectroscopic Analysis

Cancers ◽

10.3390/cancers12071708 ◽

2020 ◽

Vol 12 (7) ◽

pp. 1708 ◽

Cited By ~ 1

Author(s):

Hemendra Ghimire ◽

Chakravarthy Garlapati ◽

Emiel A. M. Janssen ◽

Uma Krishnamurti ◽

Gengsheng Qin ◽

...

Keyword(s):

Breast Cancer ◽

Infrared Spectroscopy ◽

Sensitivity And Specificity ◽

Conformational Changes ◽

Structural Changes ◽

Breast Cancer Patients ◽

Serum Samples ◽

Structural Alterations ◽

Dna And Rna ◽

Α Helix

Protein structural alterations, including misfolding and aggregation, are a hallmark of several diseases, including cancer. However, the possible clinical application of protein conformational analysis using infrared spectroscopy to detect cancer-associated structural changes in proteins has not been established yet. The present study investigates the applicability of Fourier transform infrared spectroscopy in distinguishing the sera of healthy individuals and breast cancer patients. The cancer-associated alterations in the protein structure were analyzed by fitting the amide I (1600–1700 cm−1) band of experimental curves, as well as by comparing the ratio of the absorbance values at the amide II and amide III bands, assigning those as the infrared spectral signatures. The snapshot of the breast cancer-associated alteration in circulating DNA and RNA was also evaluated by extending the spectral fitting protocol to the complex region of carbohydrates and nucleic acids, 1140–1000 cm−1. The sensitivity and specificity of these signatures, representing the ratio of the α-helix and β-pleated sheet in proteins, were both 90%. Likewise, the ratio of amides II and amide III (I1556/I1295) had a sensitivity and specificity of 100% and 80%, respectively. Thus, infrared spectroscopy can serve as a powerful tool to understand the protein structural alterations besides distinguishing breast cancer and healthy serum samples.

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Cryo-EM structures of HIV-1 trimer bound to CD4-mimetics BNM-III-170 and M48U1 adopt a CD4-bound open conformation

Nature Communications ◽

10.1038/s41467-021-21816-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Claudia A. Jette ◽

Christopher O. Barnes ◽

Sharon M. Kirk ◽

Bruno Melillo ◽

Amos B. Smith ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Membrane Fusion ◽

Conformational Changes ◽

Structural Changes ◽

Target Cells ◽

Helical Bundle ◽

Open Conformation ◽

Immunodeficiency Virus ◽

Hiv 1 ◽

Human Immunodeficiency Virus 1

AbstractHuman immunodeficiency virus-1 (HIV-1), the causative agent of AIDS, impacts millions of people. Entry into target cells is mediated by the HIV-1 envelope (Env) glycoprotein interacting with host receptor CD4, which triggers conformational changes allowing binding to a coreceptor and subsequent membrane fusion. Small molecule or peptide CD4-mimetic drugs mimic CD4’s Phe43 interaction with Env by inserting into the conserved Phe43 pocket on Env subunit gp120. Here, we present single-particle cryo-EM structures of CD4-mimetics BNM-III-170 and M48U1 bound to a BG505 native-like Env trimer plus the CD4-induced antibody 17b at 3.7 Å and 3.9 Å resolution, respectively. CD4-mimetic-bound BG505 exhibits canonical CD4-induced conformational changes including trimer opening, formation of the 4-stranded gp120 bridging sheet, displacement of the V1V2 loop, and formation of a compact and elongated gp41 HR1C helical bundle. We conclude that CD4-induced structural changes on both gp120 and gp41 Env subunits are induced by binding to the gp120 Phe43 pocket.

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Structural basis for two-way communication between dynein and microtubules

10.1101/774414 ◽

2019 ◽

Author(s):

Noritaka Nishida ◽

Yuta Komori ◽

Osamu Takarada ◽

Atsushi Watanabe ◽

Satoko Tamura ◽

...

Keyword(s):

Disulfide Bond ◽

Conformational Changes ◽

Structural Changes ◽

Coiled Coil ◽

Cytoplasmic Dynein ◽

Structural Basis ◽

Atpase Domain ◽

Directional Bias ◽

Α Helix ◽

Half Turn

AbstractThe movements of cytoplasmic dynein on microtubule (MT) tracks is achieved by two-way communication between the microtubule-binding domain (MTBD) and the ATPase domain of dynein via an a-helical coiled-coil stalk, but the structural basis of this communication remains elusive. Here, we regulated MTBD either in high-affinity or low-affinity states by introducing a disulfide bond between the coiled-coils and analyzed the resulting structures by NMRand cryo-EM. In the MT-unbound state, the affinity changes of MTBD were achieved by sliding of the N-terminal α-helix by one half-turn, which suggests that structural changes propagate from the ATPase-domain to MTBD. In addition, cryo-EM analysis showed that MT binding induced further sliding of the N-terminal α-helix even without the disulfide bond, which suggests the MT-induced conformational changes propagate toward the ATPase domain. Based on differences in the MT-binding surface between the high- and low-affinity states, we propose a potential mechanism for the directional bias of dynein movement on MT tracks.

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Alteration of Substrate-Induced Conformational Changes of Escherichia coli Melibiose Permease by Mutating Arg149

10.1101/2020.05.31.125815 ◽

2020 ◽

Author(s):

Yibin Lin

Keyword(s):

Escherichia Coli ◽

Conformational Changes ◽

Structural Changes ◽

Spectroscopic Techniques ◽

Difference Spectroscopy ◽

Difference Spectra ◽

Binding Properties ◽

Structure Changes ◽

Β Sheets ◽

Α Helix

AbstractFourier transform infrared difference spectroscopy and fluorescence spectroscopic techniques have been used to obtain information about substrate-induced structural changes of the melibiose permease mutant R149C, compared with the Cys-less, which were reconstituted into liposomes. ATR-FTIR evidences show that Na+-induced difference spectra of R149C and Cys-less are similar. However, Na+ induces some new peaks for R149C mutant permease. This means that replacement of Arg-149 by Cys may affect the structure of MelB, and then affect the binding of Na+. Melibiose-induced difference spectra of R149C in the presence of Na+ show some peaks in the amide I region not seen in Cys-less, corresponding to turns, β-sheets, α-helix changes. This suggests that R149C mutant permease undergo some different secondary structure changes compared to Cys-less mutant permease, when binding melibiose. Comparison of the permease intrinsic fluorescence variations of R149C and Cys-less indicate that there are similar substrate binding properties between R149C and Cys-less. When analyzing the effects of different sugars it appears that the R149C mutant is more sensitive to the sugar. All these data indicate that replacement of Arg-149 by Cys will affect Na+ and sugar binding, and enhance the selectivity and sensitivity to sugars.

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Protein-induced conformational changes in 16S rRNA during assembly of the Escherichia Coli 30S ribosomal subunit: A STEM study

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100128833 ◽

1987 ◽

Vol 45 ◽

pp. 910-911

Author(s):

M. Boublik ◽

V. Mandiyan ◽

J.F. Hainfeld ◽

J.S. Wall

Keyword(s):

16S Rrna ◽

Conformational Changes ◽

Ribosomal Proteins ◽

Structural Changes ◽

Ribosomal Subunit ◽

Compact Structure ◽

E Coli ◽

Freeze Dried ◽

16S Rna ◽

30S Subunit

The aim of this study is to understand the mechanism of 16S rRNA folding into the compact structure of the small 30S subunit of E. coli ribosome. The assembly of the 30S E. coli ribosomal subunit is a sequence of specific interactions of 16S rRNA with 21 ribosomal proteins (S1-S21). Using dedicated high resolution STEM we have monitored structural changes induced in 16S rRNA by the proteins S4, S8, S15 and S20 which are involved in the initial steps of 30S subunit assembly. S4 is the first protein to bind directly and stoichiometrically to 16S rRNA. Direct binding also occurs individually between 16S RNA and S8 and S15. However, binding of S20 requires the presence of S4 and S8. The RNA-protein complexes are prepared by the standard reconstitution procedure, dialyzed against 60 mM KCl, 2 mM Mg(OAc)2, 10 mM-Hepes-KOH pH 7.5 (Buffer A), freeze-dried and observed unstained in dark field at -160°.

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Influence of Ascorbic Acid on the Structure and Function of Alpha-2- macroglobulin: Investigations using Spectroscopic and Thermodynamic Techniques

Protein and Peptide Letters ◽

10.2174/0929866526666191002113525 ◽

2020 ◽

Vol 27 (3) ◽

pp. 201-209

Author(s):

Syed Saqib Ali ◽

Mohammad Khalid Zia ◽

Tooba Siddiqui ◽

Haseeb Ahsan ◽

Fahim Halim Khan

Keyword(s):

Ascorbic Acid ◽

Conformational Changes ◽

Structural Changes ◽

The Body ◽

Titration Calorimetry ◽

Spectroscopic Techniques ◽

Human Beings ◽

Plasma Ascorbic Acid ◽

Dietary Antioxidant ◽

And Function

Background: Ascorbic acid is a classic dietary antioxidant which plays an important role in the body of human beings. It is commonly found in various foods as well as taken as dietary supplement. Objective: The plasma ascorbic acid concentration may range from low, as in chronic or acute oxidative stress to high if delivered intravenously during cancer treatment. Sheep alpha-2- macroglobulin (α2M), a human α2M homologue is a large tetrameric glycoprotein of 630 kDa with antiproteinase activity, found in sheep’s blood. Methods: In the present study, the interaction of ascorbic acid with alpha-2-macroglobulin was explored in the presence of visible light by utilizing various spectroscopic techniques and isothermal titration calorimetry (ITC). Results: UV-vis and fluorescence spectroscopy suggests the formation of a complex between ascorbic acid and α2M apparent by increased absorbance and decreased fluorescence. Secondary structural changes in the α2M were investigated by CD and FT-IR spectroscopy. Our findings suggest the induction of subtle conformational changes in α2M induced by ascorbic acid. Thermodynamics signatures of ascorbic acid and α2M interaction indicate that the binding is an enthalpy-driven process. Conclusion: It is possible that ascorbic acid binds and compromises antiproteinase activity of α2M by inducing changes in the secondary structure of the protein.

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Structural and Technological Approach to Reveal the Role of the Lipid Phase in the Formation of Soy Emulsion Gels with Chia Oil

Gels ◽

10.3390/gels7020048 ◽

2021 ◽

Vol 7 (2) ◽

pp. 48

Author(s):

Ana M. Herrero ◽

Claudia Ruiz-Capillas

Keyword(s):

Raman Spectroscopy ◽

Structural Properties ◽

Structural Changes ◽

Protein Secondary Structure ◽

Lipid Phase ◽

Α Helix ◽

Β Sheet ◽

Shed Light ◽

Chia Oil

Considerable attention has been paid to emulsion gels (EGs) in recent years due to their interesting applications in food. The aim of this work is to shed light on the role played by chia oil in the technological and structural properties of EGs made from soy protein isolates (SPI) and alginate. Two systems were studied: oil-free SPI gels (SPI/G) and the corresponding SPI EGs (SPI/EG) that contain chia oil. The proximate composition, technological properties (syneresis, pH, color and texture) and structural properties using Raman spectroscopy were determined for SPI/G and SPI/EG. No noticeable (p > 0.05) syneresis was observed in either sample. The pH values were similar (p > 0.05) for SPI/G and SPI/EG, but their texture and color differed significantly depending on the presence of chia oil. SPI/EG featured significantly lower redness and more lightness and yellowness and exhibited greater puncture and gel strengths than SPI/G. Raman spectroscopy revealed significant changes in the protein secondary structure, i.e., higher (p < 0.05) α-helix and lower (p < 0.05) β-sheet, turn and unordered structures, after the incorporation of chia oil to form the corresponding SPI/EG. Apparently, there is a correlation between these structural changes and the textural modifications observed.

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The key amino acids of E protein involved in early flavivirus infection: viral entry

Virology Journal ◽

10.1186/s12985-021-01611-2 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Tao Hu ◽

Zhen Wu ◽

Shaoxiong Wu ◽

Shun Chen ◽

Anchun Cheng

Keyword(s):

Amino Acids ◽

Conformational Changes ◽

Viral Entry ◽

Envelope Protein ◽

Cell Attachment ◽

Envelope Proteins ◽

Infection Process ◽

Early Infection ◽

Protein Amino Acids ◽

Α Helix

AbstractFlaviviruses are enveloped viruses that infect multiple hosts. Envelope proteins are the outermost proteins in the structure of flaviviruses and mediate viral infection. Studies indicate that flaviviruses mainly use envelope proteins to bind to cell attachment receptors and endocytic receptors for the entry step. Here, we present current findings regarding key envelope protein amino acids that participate in the flavivirus early infection process. Among these sites, most are located in special positions of the protein structure, such as the α-helix in the stem region and the hinge region between domains I and II, motifs that potentially affect the interaction between different domains. Some of these sites are located in positions involved in conformational changes in envelope proteins. In summary, we summarize and discuss the key envelope protein residues that affect the entry process of flaviviruses, including the process of their discovery and the mechanisms that affect early infection.

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Metastability in Monolayer Films Transferred onto Solid Substrates by the Langmuir-Blodgett Method: IR Evidence for Transfer-Induced Phase Transitions

Applied Spectroscopy ◽

10.1366/0003702944027309 ◽

1994 ◽

Vol 48 (10) ◽

pp. 1196-1203 ◽

Cited By ~ 18

Author(s):

Fazale R. Rana ◽

Suci Widayati ◽

Brian W. Gregory ◽

Richard A. Dluhy

Keyword(s):

Fatty Acid ◽

Conformational Changes ◽

Structural Changes ◽

High Surface ◽

Solid Substrate ◽

Water Interface ◽

Monolayer Films ◽

Langmuir Blodgett ◽

Monomolecular Film ◽

Air Water Interface

The rate at which a monomolecular film is deposited onto a solid substrate in the Langmuir-Blodgett process of preparing supported monolayer films influences the final structure of the transferred film. Attenuated total reflectance infrared spectroscopic studies of monolayers transferred to germanium substrates show that the speed at which the substrate is drawn through the air/water interface influences the final conformation in the hydrocarbon chains of amphiphilic film molecules. This transfer-induced effect is especially evident when the monolayer is transferred from the expanded region of surface-pressure-molecular-area isotherms at low surface pressures; the effect is minimized when the film molecules are transferred from condensed phases at high surface pressures. This phenomenon has been observed for both a fatty acid and a phospholipid, which suggests that these conformational changes may occur in a variety of hydrocarbon amphiphiles transferred from the air/water interface. This conformational ordering may be due to a kinetically limited phase transition taking place in the meniscus formed between the solid substrate and aqueous subphase. In addition, the results obtained for both the phospholipid and fatty acid suggest that the structure of the amphiphile may help determine the extent and nature of the transfer-speed-induced structural changes taking place in the monomolecular film.

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