scholarly journals Burn-related Collagen Conformational Changes in ex vivo Porcine Skin using Raman Spectroscopy

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Hanglin Ye ◽  
Rahul ◽  
Uwe Kruger ◽  
Tianmeng Wang ◽  
Sufei Shi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Raman Spectroscopy ◽  
Secondary Structure ◽  
Conformational Changes ◽  
Structural Changes ◽  
Mechanical Response ◽  
Ex Vivo ◽  
Burn Severity ◽  
Porcine Skin ◽  
Disordered Structures

AbstractThis study utilizes Raman spectroscopy to analyze the burn-induced collagen conformational changes in ex vivo porcine skin tissue. Raman spectra of wavenumbers 500–2000 cm−1 were measured for unburnt skin as well as four different burn conditions: (i) 200 °F for 10 s, (ii) 200 °F for the 30 s, (iii) 450 °F for 10 s and (iv) 450 °F for 30 s. The overall spectra reveal that protein and amino acids-related bands have manifested structural changes including the destruction of protein-related functional groups, and transformation from α-helical to disordered structures which are correlated with increasing burn severity. The deconvolution of the amide I region (1580–1720 cm−1) and the analysis of the sub-bands reveal a change of the secondary structure of the collagen from the α-like helix dominated to the β-aggregate dominated one. Such conformational changes may explain the softening of mechanical response in burnt tissues reported in the literature.

scholarly journals SERS study on myeloperoxidase and its immunocomplex: Identification of binding interactions

2010 ◽  
Vol 24 (3-4) ◽  
pp. 183-190
Author(s):  
Elisabeth S. Papazoglou ◽  
Sundar Babu ◽  
David R. Hansberry ◽  
Sakya Mohapatra ◽  
Chirag Patel
Keyword(s):  
Amino Acids ◽  
Raman Spectroscopy ◽  
Conformational Changes ◽  
Surface Enhanced Raman Spectroscopy ◽  
Biological Molecules ◽  
Sers Spectrum ◽  
Amino Acid Residues ◽  
Igg Antibodies ◽  
Surface Enhanced ◽  
Surface Enhanced Raman

Surface Enhanced Raman Spectroscopy (SERS) has demonstrated significant benefit in the identification of biological molecules. In this paper we have examined how to identify and differentiate the 150 kDa protein myeloperoxidase (MPO) from its corresponding antibody (Ab) and their immunocomplex through the use of SERS. The SERS signal of these biological molecules was enabled by 40 nm gold nanoparticles. The SERS spectra for both MPO and the Ab (an IgG molecule) demonstrated results consistent with previous published work on the Raman spectra of MPO and IgG antibodies. The immunocomplex SERS spectra showed peak shifts and intensity variations that could be attributed to conformational changes that occur during immunocomplex formation. Several key spectral areas have been identified which correspond to specific amino acids being shielded from undergoing resonance while new amino acid residues are made visible in the SERS spectrum of the immunocomplex and could be a result of conformational binding. These results indicate that SERS can be used to identify binding events and distinguish an immunocomplex from its individual components.

scholarly journals Force transduction creates long-ranged coupling in ribosomes stalled by arrest peptides

2020 ◽  
Author(s):  
Matthew H Zimmer ◽  
Michiel JM Niesen ◽  
Thomas F Miller
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Conformational Changes ◽  
Protein Biosynthesis ◽  
Essential Amino Acids ◽  
Structural Features ◽  
Applied Force ◽  
Catalytic Center ◽  
Force Propagation ◽  
Force Transduction

AbstractForce-sensitive arrest peptides regulate protein biosynthesis by stalling the ribosome as they are translated. Synthesis can be resumed when the nascent arrest peptide experiences a pulling force of sufficient magnitude to break the stall. Efficient stalling is dependent on the specific identity of a large number of amino acids, including amino acids which are tens of angstroms away from the peptidyl transferase center (PTC). The mechanism of force-induced restart and the role of these essential amino acids far from the PTC is currently unknown. We use hundreds of independent molecular dynamics trajectories spanning over 120 μs in combination with kinetic analysis to characterize the barriers along the force-induced restarting pathway for the arrest peptide SecM. We find that the essential amino acids far from the PTC play a major role in controlling the transduction of applied force. In successive states along the stall-breaking pathway, the applied force propagates up the nascent chain until it reaches the C-terminus of SecM and the PTC, inducing conformational changes that allow for restart of translation. A similar mechanism of force propagation through multiple states is observed in the VemP stall-breaking pathway, but secondary structure in VemP allows for heterogeneity in the order of transitions through intermediate states. Results from both arrest peptides explain how residues that are tens of angstroms away from the catalytic center of the ribosome impact stalling efficiency by mediating the response to an applied force and shielding the amino acids responsible for maintaining the stalled state of the PTC.Significance StatementAs nascent proteins are synthesized by the ribosome, their interactions with the environment can create pulling forces on the nascent protein that can be transmitted to the ribosome’s catalytic center. These forces can affect the rate and even the outcome of translation. We use simulations to characterize the pathway of force transduction along arrest peptides and discover how secondary structure in the nascent protein and its interactions with the ribosome exit tunnel impede force propagation. This explains how amino acids in arrest peptides that are tens of angstroms away from the ribosome’s catalytic center contribute to stalling, and, more broadly, suggests how structural features in the nascent protein dictate the ribosome’s ability to functionally respond to its environment.

Ligand-dependent active-site closure revealed in the crystal structure ofMycobacterium tuberculosisMenB complexed with product analogues

2014 ◽  
Vol 70 (11) ◽  
pp. 2959-2969 ◽  
Author(s):  
Haigang Song ◽  
Hoi Pang Sung ◽  
Yuk Sing Tse ◽  
Ming Jiang ◽  
Zhihong Guo
Keyword(s):  
Amino Acids ◽  
Conformational Changes ◽  
Active Site ◽  
Structural Changes ◽  
Catalytic Mechanism ◽  
Bulk Solution ◽  
Type I ◽  
Important Target ◽  
New Antibiotics ◽  
Carboxy Terminal

1,4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase catalyzes an essential intramolecular Claisen condensation in menaquinone biosynthesis and is an important target for the development of new antibiotics. This enzyme inMycobacterium tuberculosisis cofactor-free and is classified as a type II DHNA-CoA synthase, differing from type I enzymes, which rely on exogenous bicarbonate for catalysis. Its crystal structures in complex with product analogues have been determined at high resolution to reveal ligand-dependent structural changes, which include the ordering of a 27-residue active-site loop (amino acids 107–133) and the reorientation of the carboxy-terminal helix (amino acids 289–301) that forms part of the active site from the opposing subunit across the trimer–trimer interface. These structural changes result in closure of the active site to the bulk solution, which is likely to take place through an induced-fit mechanism, similar to that observed for type I DHNA-CoA synthases. These findings demonstrate that the ligand-dependent conformational changes are a conserved feature of all DHNA-CoA synthases, providing new insights into the catalytic mechanism of this essential tubercular enzyme.

scholarly journals Changes in the Structure and Digestibility of Myoglobin Treated With Sodium Chloride

2021 ◽  
Vol 5 (Supplement_2) ◽  
pp. 661-661
Author(s):  
Hui Liu ◽  
Qian Li ◽  
Chunbao Li
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Sodium Chloride ◽  
Secondary Structure ◽  
Digestive Enzymes ◽  
Structural Changes ◽  
Tertiary Structure ◽  
Dynamics Simulation ◽  
High Concentration ◽  
Salt Ions

Abstract Objectives Changes in the structure of myoglobin affect its digestibility and myoglobin can't be completely broken down of pepsin. The exact mechanism of this breakdown is not clear. It can be inferred that myoglobin is broken down into polypeptides whose structures do not fully conform to the spatial characteristics of digestive enzymes. Myoglobin dissolution in different salt concentrations and changes in secondary structure were examined by spectroscopic examination. The molecular dynamics simulation was used to study the stability of these structural changes and their combination with digestive enzymes. Finally, since the products of digestion are determined by the catalytic centers of digestive enzymes, the substrate channel is extended to study the relationship between digestive enzymes and substrates. Methods In this study, different concentrations of sodium chloride were added for a certain period of time in advance to detect changes in the secondary structure of myoglobin, leading to changes in digestibility. Myoglobin and digestive enzymes were docked for molecular dynamics simulations to analyze the energy and structural changes in the interactions between substrates and proteins. Results Salt-treated protein can affect the secondary structure changes of protein. High concentration of salt-treated protein will lead to protein aggregation and denaturation, affecting digestibility. Low concentration of salt-treated protein may lead to exposure of sleeping areas, reducing digestibility. In terms of structure, salt ions lead to changes in the bonding of amino acids in the protein and affect the substrate's entry into the enzyme activity center. Conclusions Treatment of myoglobin with different salt concentrations did not change its tertiary structure but low salt concentrations lowered its digestibility, probably due to salt ions altering a number of key amino acid bonds, making the structure more stable and less susceptible to digest. Some low molecular weight peptides remain after pepsin digestion. This may be due to the distance between the key amino acids in the active catalytic center of pepsin being insufficient to form stable conformations with small peptides. Funding Sources This work was supported by the grants from NSFC (32072211).

Classification of burn injury using Raman spectroscopy and optical coherence tomography: An ex-vivo study on porcine skin

Burns ◽  
2019 ◽  
Vol 45 (3) ◽  
pp. 659-670 ◽  
Author(s):  
Lakshmi Priya Rangaraju ◽  
Gautam Kunapuli ◽  
Dayna Every ◽  
Oscar D. Ayala ◽  
Priya Ganapathy ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Optical Coherence Tomography ◽  
Burn Injury ◽  
Ex Vivo ◽  
Optical Coherence ◽  
Porcine Skin ◽  
Ex Vivo Study

Raman spectroscopy accurately classifies burn severity in an ex vivo model

Burns ◽  
2020 ◽  
Author(s):  
Hanglin Ye ◽  
Rahul ◽  
Uwe Kruger ◽  
Tianmeng Wang ◽  
Sufei Shi ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Ex Vivo ◽  
Burn Severity ◽  
Ex Vivo Model

scholarly journals Prediction of Steam Burns Severity using Raman Spectroscopy on ex vivo Porcine Skin

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Lina Zhai ◽  
Christian Adlhart ◽  
Fabrizio Spano ◽  
Riccardo Innocenti Malini ◽  
Agnieszka K. Piątek ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Ex Vivo ◽  
Porcine Skin

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

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°.

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

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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