scholarly journals Hoop-like role of the cytosolic interface helix in Vibrio PomA, an ion-conducting membrane protein, in the bacterial flagellar motor

2021 ◽  
Author(s):  
Tatsuro Nishikino ◽  
Yugo Sagara ◽  
Hiroyuki Terashima ◽  
Michio Homma ◽  
Seiji Kojima
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Growth Defect ◽  
Flagellar Motor ◽  
Inner Membrane ◽  
Assembly Mechanism ◽  
Conduction Pathway ◽  
Ion Conducting ◽  
The Stability

Vibrio has a polar flagellum driven by sodium ions for swimming. The force-generating stator unit consists of PomA and PomB. PomA contains four-transmembrane regions and a cytoplasmic domain of approximately 100 residues which interacts with the rotor protein, FliG, to be important for the force generation of rotation. The three-dimensional structure of the stator shows that the cytosolicinterface (CI) helix of PomA is located parallel to the inner membrane. In this study, we investigated the function of CI helix and its role as stator. Systematic proline mutagenesis showed that residues K64, F66, and M67 were important for this function. The mutant stators did not assemble around the rotor. Moreover, the growth defect caused by PomB plug deletion was suppressed by these mutations. We speculate that the mutations affect the structure of the helices extending from TM3 and TM4 and reduce the structural stability of the stator complex. This study suggests that the helices parallel to the inner membrane play important roles in various processes, such as the hoop-like function in securing the stability of the stator complex and the ion conduction pathway, which may lead to the elucidation of the ion permeation and assembly mechanism of the stator.

scholarly journals Analysis of structural similarities between brain Thy-1 antigen and immunoglobulin domains. Evidence for an evolutionary relationship and a hypothesis for its functional significance

1981 ◽  
Vol 195 (1) ◽  
pp. 31-40 ◽  
Author(s):  
F E Cohen ◽  
J Novotný ◽  
M J E Sternberg ◽  
D G Campbell ◽  
A F Williams
Keyword(s):  
Functional Significance ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Evolutionary Relationship ◽  
Dimensional Structure ◽  
Sequence Homologies ◽  
Beta Structure ◽  
Beta 2 Microglobulin

The Thy-1 membrane glycoprotein from rat brain is shown to have structural and sequence homologies with immunoglobulin (Ig) domains on the basis of the following evidence. 1. The two disulphide bonds of Thy-1 are both consistent with the Ig-fold. 2. The molecule contains extensive beta-structure as shown by the c.d. spectrum. 3. Secondary structure prediction locates beta-strands along the sequence in a manner consistent with the Ig-fold. 4. On the basis of rules derived from known beta-sheet structures, a three-dimensional structure with the Ig-fold is predicted as favourable for Thy-1. 5. Sequences in the proposed beta-strands of Thy-1 and known beta-strands of Ig domains show significant sequence homology. This homology is statistically more significant than for the comparison of proposed beta-strand sequences of beta 2-microglobulin with Ig domains. An hypothesis is presented for the possible functional significance of an evolutionary relationship between Thy-1 and Ig. It is suggested that both Thy-1 and Ig evolved from primitive molecules, with an Ig fold, which mediated cell--cell interactions. The present-day role of Thy-1 may be similar to that of the primitive domain.

3D Structure of Striations in the North Pacific

2021 ◽  
Author(s):  
YU ZHANG ◽  
YU PING GUAN ◽  
RUI XIN HUANG
Keyword(s):  
North Pacific ◽  
3D Structure ◽  
Three Dimensional ◽  
Vertical Plane ◽  
Dimensional Structure ◽  
The North ◽  
Layer Analysis ◽  
Fluid Potential ◽  
The North Pacific

AbstractOcean striations are composed of alternating quasi-zonal band-like flows; this kind of organized structure of currents be found in all world’s oceans and seas. Previous studies have mainly been focused on the mechanisms of their generation and propagation. This study uses the spatial high-pass filtering to obtain the three-dimensional structure of ocean striations in the North Pacific in both the z-coordinate and σ-coordinate based on 10-yr averaged SODA3 data. First, we identify an ideal-fluid potential density domain where the striations are undisturbed by the surface forcing and boundary effects. Second, using the isopycnal layer analysis, we show that on isopycnal surfaces the orientations of striations nearly follow the potential vorticity (PV) contours, while in the meridional-vertical plane the central positions of striations are generally aligned with the latitude of zero gradient of the relative PV. Our analysis provides a simple dynamical interpretation and better understanding for the role of ocean striations.

scholarly journals The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
Author(s):  
Antonio PÁRRAGA ◽  
Isabel GARCÍA-SÁEZ ◽  
Sinead B. WALSH ◽  
Timothy J. MANTLE ◽  
Miquel COLL
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Glutathione S Transferase ◽  
X Ray ◽  
The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

Protein intrachain contact prediction with most interacting residues (MIR)

2014 ◽  
Vol 10 (4) ◽  
Author(s):  
Ruben Acuña ◽  
Zoé Lacroix ◽  
Nikolaos Papandreou ◽  
Jacques Chomilier
Keyword(s):  
Structural Changes ◽  
Hydrophobic Interactions ◽  
Three Dimensional ◽  
Accessible Surface Area ◽  
Dimensional Structure ◽  
Closed Loops ◽  
Folding Process ◽  
Folding Nucleus ◽  
Accessible Surface ◽  
The Stability

AbstractThe transition state ensemble during the folding process of globular proteins occurs when a sufficient number of intrachain contacts are formed, mainly, but not exclusively, due to hydrophobic interactions. These contacts are related to the folding nucleus, and they contribute to the stability of the native structure, although they may disappear after the energetic barrier of transition states has been passed. A number of structure and sequence analyses, as well as protein engineering studies, have shown that the signature of the folding nucleus is surprisingly present in the native three-dimensional structure, in the form of closed loops, and also in the early folding events. These findings support the idea that the residues of the folding nucleus become buried in the very first folding events, therefore helping the formation of closed loops that act as anchor structures, speed up the process, and overcome the Levinthal paradox. We present here a review of an algorithm intended to simulate in a discrete space the early steps of the folding process. It is based on a Monte Carlo simulation where perturbations, or moves, are randomly applied to residues within a sequence. In contrast with many technically similar approaches, this model does not intend to fold the protein but to calculate the number of non-covalent neighbors of each residue, during the early steps of the folding process. Amino acids along the sequence are categorized as most interacting residues (MIRs) or least interacting residues. The MIR method can be applied under a variety of circumstances. In the cases tested thus far, MIR has successfully identified the exact residue whose mutation causes a switch in conformation. This follows with the idea that MIR identifies residues that are important in the folding process. Most MIR positions correspond to hydrophobic residues; correspondingly, MIRs have zero or very low accessible surface area. Alongside the review of the MIR method, we present a new postprocessing method called smoothed MIR (SMIR), which refines the original MIR method by exploiting the knowledge of residue hydrophobicity. We review known results and present new ones, focusing on the ability of MIR to predict structural changes, secondary structure, and the improved precision with the SMIR method.

Role of LHCII-containing macrodomains in the structure, function and dynamics of grana

2000 ◽  
Vol 27 (3) ◽  
pp. 279 ◽  
Author(s):  
G. Garab ◽  
L. Mustárdy
Keyword(s):  
Excitation Energy ◽  
Long Range ◽  
Structural Changes ◽  
Higher Plants ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Lateral Heterogeneity ◽  
Long Distance ◽  
3D Network

In higher plants and green algae two types of thylakoids are distinguished, granum (stacked) and stroma (unstacked) thylakoids. They form a three-dimensional (3D) network with large lateral heterogeneity: photosystem II (PSII) and the associated main chlorophyll a/b light-harvesting complex (LHCII) are found predominantly in the stacked region, while PSI and LHCI are located mainly in the unstacked region of the membrane. This picture emerged from the discovery of the physical separation of the two photosystems (Boardman and Anderson 1964). Granal chloroplasts possess significant flexibility, which is essential for optimizing the photosynthetic machinery under various environmental conditions. However, our understanding concerning the assembly, structural dynamics and regulatory functions of grana is far from being complete. In this paper we overview the significance of the three-dimensional structure of grana in the absorption properties, ionic equilibrations, and in the diffusion of membrane components between the stacked and unstacked regions. Further, we discuss the role of chiral macrodomains in the grana. Lateral heterogeneity of thylakoid membranes is proposed to be a consequence of the formation of macrodomains constituted of LHCII and PSII; their long range order permits long distance migration of excitation energy, which explains the energetic connectivity of PSII particles. The ability of macrodomains to undergo light-induced reversible structural changes lends structural flexibility to the granum. In purified LHCII, which has also been shown to form stacked lamellar aggregates with long range chiral order, excitation energy migrates for large distances; these macroaggregates are also capable of undergoing light-induced reversible structural changes and fluorescence quenching. Hence, some basic properties of grana appear to originate from its main constituent, the LHCII.

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

scholarly journals Solution structure of the strawberry allergen Fra a 1

2012 ◽  
Vol 32 (6) ◽  
pp. 567-575 ◽  
Author(s):  
Christian Seutter von Loetzen ◽  
Kristian Schweimer ◽  
Wilfried Schwab ◽  
Paul Rösch ◽  
Olivia Hartl-Spiegelhauer
Keyword(s):  
Solution Structure ◽  
Three Dimensional ◽  
Protein Family ◽  
Dimensional Structure ◽  
Hydrophobic Pocket ◽  
Pigment Synthesis ◽  
Family Protein ◽  
Pr10 Protein ◽  
Α Helix

The PR10 family protein Fra a 1E from strawberry (Fragaria x ananassa) is down-regulated in white strawberry mutants, and transient RNAi (RNA interference)-mediated silencing experiments confirmed that Fra a 1 is involved in fruit pigment synthesis. In the present study, we determined the solution structure of Fra a 1E. The protein fold is identical with that of other members of the PR10 protein family and consists of a seven-stranded antiparallel β-sheet, two short V-shaped α-helices and a long C-terminal α-helix that encompass a hydrophobic pocket. Whereas Fra a 1E contains the glycine-rich loop that is highly conserved throughout the protein family, the volume of the hydrophobic pocket and the size of its entrance are much larger than expected. The three-dimensional structure may shed some light on its physiological function and may help to further understand the role of PR10 proteins in plants.

Sign in / Sign up

Export Citation Format

Share Document