scholarly journals Mutational Analysis of Transmembrane Regions 3 and 4 of SecY, a Central Component of Protein Translocase

2004 ◽  
Vol 186 (12) ◽  
pp. 3960-3969 ◽  
Author(s):  
Hiroyuki Mori ◽  
Naomi Shimokawa ◽  
Yasunari Satoh ◽  
Koreaki Ito
Keyword(s):  
Mutational Analysis ◽  
Protein Translocation ◽  
Structural Information ◽  
Synthetic Lethality ◽  
Contact Point ◽  
Alpha Helix ◽  
Growth Defect ◽  
Central Component ◽  
Contact Points ◽  
Specific Contact

ABSTRACT The SecYEG heterotrimeric membrane protein complex functions as a channel for protein translocation across the Escherichia coli cytoplasmic membrane. SecY is the central subunit of the SecYEG complex and contains 10 transmembrane segments (TM1 to TM10). Previous mutation studies suggested that TM3 and TM4 are particularly important for SecY function. To further characterize TM3 and TM4, we introduced a series of cysteine-scanning mutations into these segments. With one exception (an unstable product), all the mutant proteins complemented the cold-sensitive growth defect of the secY39 mutant. A combination of this secY mutation and the secG deletion resulted in synthetic lethality, and the TM3 and TM4 SecY cysteine substitution mutations were examined for their ability to complement this lethality. Although they were all positive for complementation, some of the complemented cells exhibited significant retardation of protein export. The substitution-sensitive residues in TM3 can be aligned to one side of the alpha-helix, and those in TM4 revealed a tendency for residues closer to the cytosolic side of the membrane to be more severely affected. Disulfide cross-linking experiments identified a specific contact point for TM3 and SecG TM2 as well as for TM4 and SecG TM1. Thus, although TM3 and TM4 do not contain any single residue that is absolutely required, they include functionally important helix surfaces and specific contact points with SecG. These results are discussed in light of the structural information available for the SecY complex.

scholarly journals Slipping–rolling transitions of a body with two contact points

2021 ◽  
Author(s):  
Mate Antali ◽  
Gabor Stepan
Keyword(s):  
Rigid Body ◽  
Contact Point ◽  
Static Friction ◽  
Rigid Body Dynamics ◽  
Contact Forces ◽  
Friction Forces ◽  
Contact Points ◽  
Body Dynamics ◽  
Coulomb Model ◽  
Rigid Surfaces

AbstractIn this paper, the general kinematics and dynamics of a rigid body is analysed, which is in contact with two rigid surfaces in the presence of dry friction. Due to the rolling or slipping state at each contact point, four kinematic scenarios occur. In the two-point rolling case, the contact forces are undetermined; consequently, the condition of the static friction forces cannot be checked from the Coulomb model to decide whether two-point rolling is possible. However, this issue can be resolved within the scope of rigid body dynamics by analysing the nonsmooth vector field of the system at the possible transitions between slipping and rolling. Based on the concept of limit directions of codimension-2 discontinuities, a method is presented to determine the conditions when the two-point rolling is realizable without slipping.

scholarly journals Cavitation between cylinder-liner and piston-ring in a new designed optical IC engine

2021 ◽  
pp. 146808742110080
Author(s):  
Jamshid Malekmohammadi Nouri ◽  
Ioannis Vasilakos ◽  
Youyou Yan
Keyword(s):  
High Speed ◽  
Contact Point ◽  
Cylinder Liner ◽  
Optical Methods ◽  
Engine Management System ◽  
Great Success ◽  
Ic Engine ◽  
Contact Points ◽  
Lubricant Flow ◽  
Cavitation Intensity

A new engine block with optical access has been designed and manufactured capable of running up to 3000 r/min with the same specification as the unmodified engine. The optical window allowed access to the full length of the liner over a width of 25 mm to investigate the lubricant flow and cavitation at contact point between the rings and cylinder-liner. In addition, it allowed good access into the combustion chamber to allow charged flow, spray and combustion visualisation and measurements using different optical methods. New custom engine management system with build in LabView allowed for the precise full control of the engine. The design of the new optical engine was a great success in producing high quality images of lubricant flow, cavitation formation and development at contact point at different engine speeds ranging from 208 to 3000 r/min and lubricant temperatures (30°C–70°C) using a high-speed camera. The results under motorised operation confirmed that there was no cavitation at contact points during the intake/exhaust strokes due to low in-cylinder presure, while during compression/expansion strokes, with high in-cylinder pressure, considerable cavities were observed, in particular, during the compression stroke. Lubricant temperatures had the effect of promoting cavities both in their intensity and covered ring area up to 50°C as expected. Beyond that, although the cavitation intensity increases further with temperature, its area reduces due to possible collapse of the cavitating bubbles at higher temperature. The change of engine speed from 208 to 800 r/min increased cavitating area considerably by 52% of the ring area and was further increased by 19% at 1000 r/min. After that, the results showed very small increase in cavitation area (1.3% at 2000 r/min) with similar intensity and distribution across the ring.

scholarly journals The HeLa Pur factor binds single-stranded DNA at a specific element conserved in gene flanking regions and origins of DNA replication.

1992 ◽  
Vol 12 (3) ◽  
pp. 1257-1265 ◽  
Author(s):  
A D Bergemann ◽  
E M Johnson
Keyword(s):  
Dna Replication ◽  
Consensus Sequence ◽  
Specific Element ◽  
Contact Points ◽  
Nuclear Extracts ◽  
Specific Contact ◽  
Myc Gene ◽  
Specific Affinity ◽  
Initiation Of Dna Replication ◽  
Flanking Regions

A major site of DNA bending is located 1.6 kb upstream of the P1 transcription start site of the human c-myc gene, near the center of a reported zone of initiation of DNA replication. A repeated, purine-rich element, termed PUR, at the bend site is specifically bound by a protein in HeLa cell nuclear extracts. This protein has specific affinity for the purine-rich single strand of the element. Methylation interference maps a pattern of specific contact points with guanosine bases in a 24-mer oligonucleotide containing the element. UV cross-linking reveals that contact is made by a polypeptide of approximately 28 kDa. The PUR element is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. The consensus sequence GGNNGAGGGAGARRRR has been derived. This element is present near centers of regions of two mammalian loci (human c-myc and hamster dhfr) recently reported as initiation zones for DNA replication. A 24-mer oligonucleotide representing the hamster dhfr version of the PUR element effectively competes with the human c-myc version for binding to Pur.

scholarly journals The macroscopic shape of assemblies formed from microparticles based on host–guest interaction dependent on the guest content

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Takahiro Itami ◽  
Akihito Hashidzume ◽  
Yuri Kamon ◽  
Hiroyasu Yamaguchi ◽  
Akira Harada
Keyword(s):  
Molecular Recognition ◽  
Smart Materials ◽  
Self Assembly ◽  
Early Stage ◽  
Contact Point ◽  
Sodium Acrylate ◽  
Contact Points ◽  
Assembly Behavior ◽  
Small Clusters ◽  
Macroscopic Shape

AbstractBiological macroscopic assemblies have inspired researchers to utilize molecular recognition to develop smart materials in these decades. Recently, macroscopic self-assemblies based on molecular recognition have been realized using millimeter-scale hydrogel pieces possessing molecular recognition moieties. During the study on macroscopic self-assembly based on molecular recognition, we noticed that the shape of assemblies might be dependent on the host–guest pair. In this study, we were thus motivated to study the macroscopic shape of assemblies formed through host–guest interaction. We modified crosslinked poly(sodium acrylate) microparticles, i.e., superabsorbent polymer (SAP) microparticles, with β-cyclodextrin (βCD) and adamantyl (Ad) residues (βCD(x)-SAP and Ad(y)-SAP microparticles, respectively, where x and y denote the mol% contents of βCD and Ad residues). Then, we studied the self-assembly behavior of βCD(x)-SAP and Ad(y)-SAP microparticles through the complexation of βCD with Ad residues. There was a threshold of the βCD content in βCD(x)-SAP microparticles for assembly formation between x = 22.3 and 26.7. On the other hand, the shape of assemblies was dependent on the Ad content, y; More elongated assemblies were formed at a higher y. This may be because, at a higher y, small clusters formed in an early stage can stick together even upon collisions at a single contact point to form elongated aggregates, whereas, at a smaller y, small clusters stick together only upon collisions at multiple contact points to give rather circular assemblies. On the basis of these observations, the shape of assembly formed from microparticles can be controlled by varying y.

scholarly journals Identification of the bud emergence gene BEM4 and its interactions with rho-type GTPases in Saccharomyces cerevisiae.

1996 ◽  
Vol 16 (8) ◽  
pp. 4387-4395 ◽  
Author(s):  
D Mack ◽  
K Nishimura ◽  
B K Dennehey ◽  
T Arbogast ◽  
J Parkinson ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Synthetic Lethality ◽  
Cell Polarization ◽  
Growth Defect ◽  
Nucleotide Exchange ◽  
Loss Of Function ◽  
Multicopy Suppressor ◽  
Bud Emergence ◽  
Multicopy Suppressors ◽  
Multiple Copies

The Rho-type GTPase Cdc42p is required for cell polarization and bud emergence in Saccharomyces cerevisiae. To identify genes whose functions are linked to CDC42, we screened for (i) multicopy suppressors of a Ts- cdc42 mutant, (ii) mutants that require multiple copies of CDC42 for survival, and (iii) mutations that display synthetic lethality with a partial-loss-of-function allele of CDC24, which encodes a guanine nucleotide exchange factor for Cdc42p. In all three screens, we identified a new gene, BEM4. Cells from which BEM4 was deleted were inviable at 37 degrees C. These cells became unbudded, large, and round, consistent with a model in which Bem4p acts together with Cdc42p in polarity establishment and bud emergence. In some strains, the ability of CDC42 to serve as a multicopy suppressor of the Ts- growth defect of deltabem4 cells required co-overexpression of Rho1p, which is an essential Rho-type GTPase necessary for cell wall integrity. This finding suggests that Bem4p also affects Rho1p function. Bem4p displayed two-hybrid interactions with Cdc42p, Rho1p, and two of the three other known yeast Rho-type GTPases, suggesting that Bem4p can interact with multiple Rho-type GTPases. Models for the role of Bem4p include that it serves as a chaperone or modulates the interaction of these GTPases with one or more of their targets or regulators.

Spatial Kinematic Analysis of Threaded Fastener Assembly

2005 ◽  
Vol 128 (1) ◽  
pp. 116-127 ◽  
Author(s):  
Stephen Wiedmann ◽  
Bob Sturges
Keyword(s):  
Design Space ◽  
Compliant Mechanisms ◽  
Contact Point ◽  
Three Dimensional ◽  
Vertical Movement ◽  
Initial Contact ◽  
Geometric Problem ◽  
Intelligent Sensor ◽  
Contact State ◽  
Contact Points

Compliant mechanisms for rigid part mating exist for prismatic geometries. A few instances are known of mechanisms to assemble screw threads. A comprehensive solution to this essentially geometric problem comprises at least three parts: parametric equations for nut and bolt contact in the critical starting phase of assembly, the possible space of motions between these parts during this phase, and the design space of compliant devices which accomplish the desired motions in the presence of friction and positional uncertainty. This work concentrates on the second part in which the threaded pair is modeled numerically, and contact tests are automated through software. Tessellated solid models were used during three-dimensional collision analysis to enumerate the approximate location of the initial contact point. The advent of a second contact point presented a more constrained contact state. Thus, the bolt is rotated about a vector defined by the initial two contact points until a third contact location was found. By analyzing the depth of intersection of the bolt into the nut as well as the vertical movement of the origin of the bolt reference frame, we determined that there are three types of contacts states present: unstable two-point, quasi-stable two-point, stable three point. The space of possible motions is bounded by these end conditions which will differ in detail depending upon the starting orientations. We investigated all potential orientations which obtain from a discretization of the roll, pitch, and yaw uncertainties, each of which has its own set of contact points. From this exhaustive examination, a full contact state history was determined, which lays the foundation for the design space of either compliant mechanisms or intelligent sensor-rich controls.

Multi-Agent Form Closure Capture of a Generic 2D Polygonal Object Based on Projective Path Planning

2006 ◽  
Author(s):  
Pankaj Sharma ◽  
Anupam Saxena ◽  
Ashish Dutta
Keyword(s):  
Path Planning ◽  
Contact Point ◽  
Point Contact ◽  
Object Boundary ◽  
Actual Object ◽  
Contact Points ◽  
Correct Orientation ◽  
Novel Approach ◽  
Form Closure ◽  
Multi Agent

The study of multi-agent capture and manipulation of an object has been an area of active interest for many researchers. This paper presents a novel approach using Genetic Algorithm to determine the optimal contact points and the total number of agents (mobile robots) required to capture a stationary generic 2D polygonal object. After the goal points are determined the agents then reach their respective goals using a decentralized projective path planning algorithm. Form closure of the object is obtained using the concept of accessibility angle. The object boundary is first expanded and the robots reach the expanded object goal points and then converge on the actual object. This ensures that the agents reach the actual goal points at the same time and have the correct orientation. Frictionless point contact between the object and robots is assumed. The shape of the robot is considered a circle such that it can only apply force in outward radial direction from its center and along the normal to the object boundary at the contact point. Simulations results are presented that prove the effectiveness of the proposed method.

Unraveling Paradoxical Theories for Rigid Body Collisions

1991 ◽  
Vol 58 (4) ◽  
pp. 1049-1055 ◽  
Author(s):  
W. J. Stronge
Keyword(s):  
Frictional Force ◽  
Contact Point ◽  
Tangential Velocity ◽  
Velocity Slip ◽  
Rigid Bodies ◽  
Contact Points ◽  
Before And After ◽  
Limited Applicability ◽  
Work Done ◽  
Impulsive Reaction

A collision between two rigid bodies has a normal impulsive reaction at the contact point (CP). If the bodies are slightly rough and the contact points have a relative tangential velocity (slip), there is also a frictional force that opposes slip. Small initial slip can halt before contact terminates; when slip halts the frictional force changes and the collision process is separated into periods before and after halting. An energetically consistent theory for collisions with slip that halts is based on the work done by normal (nonfrictional) forces during restitution and compression phases. This theory clearly separates dissipation due to frictional forces from that due to internal irreversible deformation. With this theory, both normal and tangential components of the impulsive reaction always dissipate energy during collisions. In contrast, Newton’s impact law results in calculations of paradoxical increases in energy for collisions where slip reverses. This law relates normal components of relative velocity for the CP at separation and incidence by a constant (the coefficient of restitution e). Newton’s impact law is a kinematic definition for e that generally depends on the slip process and friction; consequently it has limited applicability.

scholarly journals Solution structure of Gaussia Luciferase with five disulfide bonds and identification of a putative coelenterazine binding cavity by heteronuclear NMR

2020 ◽  
Author(s):  
Nan Wu ◽  
Naohiro Kobayashi ◽  
Kengo Tsuda ◽  
Satoru Unzai ◽  
Tomonori Saotome ◽  
...  
Keyword(s):  
Disulfide Bonds ◽  
Solution Structure ◽  
Heteronuclear Nmr ◽  
Structural Information ◽  
Alpha Helix ◽  
Reporter Protein ◽  
Gaussia Luciferase ◽  
Hydrophobic Cavity ◽  
Binding Cavity ◽  
Heteronuclear Multidimensional Nmr

AbstractGaussia luciferase (GLuc) is the smallest luciferase (18.2kDa; 168 residues) reported so far and is thus attracting much attention as a reporter protein, but the lack of structural information is hampering further application. Here, we report the first solution structure of a fully active, recombinant GLuc determined by heteronuclear multidimensional NMR. We obtained a natively folded GLuc by bacterial expression and efficient refolding using a solubility tag. Almost perfect assignments of GLuc’s 1H, 13C and 15N backbone signals were obtained. GLuc structure was determined using CYANA, which automatically identified over 2500 NOEs of which > 570 were long-range. GLuc is an all-alpha-helix protein made of nine helices. The region spanning residues 10–18, 36-81, 96-145 and containing eight out of the nine helices was determined with a Cα-atom RMSD of 1.39 ű 0.39 Å. The structure of GLuc is novel and unique. Two homologous sequential repeats form two anti-parallel bundles made by 4 helices and tied together by three disulfide bonds. The N-terminal helix 1 is grabbed by these 4 helices. Further, we found a hydrophobic cavity where several residues responsible for bioluminescence were identified in previous mutational studies, and we thus hypothesize that this is a catalytic cavity, where the hydrophobic coelenterazine binds and the bioluminescence reaction takes place.

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