scholarly journals Folding of Aquaporin 1: Multiple evidence that helix 3 can shift out of the membrane core

2015 ◽  
Author(s):  
Minttu T Virkki ◽  
Nitin Agrawal ◽  
Elin Edsbäcker ◽  
Susana Cristobal ◽  
Arne Elofsson ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Md Simulations ◽  
Integral Membrane Proteins ◽  
Second Step ◽  
Transmembrane Helices ◽  
Step Process ◽  
Aquaporin 1 ◽  
The Third ◽  
Rearrangement Process ◽  
Sec Translocon

The folding of most integral membrane proteins follows a two-step process: Initially, individual transmembrane helices are inserted into the membrane by the Sec translocon. Thereafter, these helices fold to shape the final conformation of the protein. However, for some proteins, including Aquaporin 1 (AQP1), the folding appears to follow a more complicated path. AQP1 has been reported to first insert as a four-helical intermediate, where helix 2 and 4 are not inserted into the membrane. In a second step this intermediate is folded into a six-helical topology. During this process, the orientation of the third helix is inverted. Here, we propose a mechanism for how this reorientation could be initiated: First, helix 3 slides out from the membrane core resulting in that the preceding loop enters the membrane. The final conformation could then be formed as helix 2, 3 and 4 are inserted into the membrane and the reentrant regions come together. We find support for the first step in this process by showing that the loop preceding helix 3 can insert into the membrane. Further, hydrophobicity curves, experimentally measured insertion efficiencies and MD-simulations suggest that the barrier between these two hydrophobic regions is relatively low, supporting the idea that helix 3 can slide out of the membrane core, initiating the rearrangement process

Beyond “No food and drink in the gallery”: Writing a best practices document for food management in museums

2016 ◽  
Vol 30 (1-2) ◽  
pp. 111-117
Author(s):  
Rebecca Newberry ◽  
Bethany Palumbo ◽  
Fran Ritchie
Keyword(s):  
Natural History ◽  
Best Practices ◽  
Best Practice ◽  
Second Step ◽  
Step Process ◽  
The Third ◽  
Preservation Methods ◽  
Food Management ◽  
The Subject ◽  
Food And Drink

Abstract In 2015, the Society for the Preservation of Natural History Collections (SPNHC) Conservation Committee created a best practices document for food management in collection-holding institutions. This paper discusses the three-step process, devised by the committee, through which this was achieved. The first step was to research existing literature on the subject. Scant results showed that a best practices document on the subject would be of great benefit to the field. The second step was to survey collection professionals. This provided the committee a stronger understanding of current food management challenges and successes, as well as topics to address in the best practices document. The third step was to gain consensus from these professionals. A draft of the document was presented at three international conferences, and feedback was incorporated into the final recommendations. The best practices document is available on the SPNHC wiki and may be updated. It is possible to write a best practice on any subject by replicating this three-step process. The Conservation Committee believes this process can be applied to other areas that are in need of new or revised preservation methods.

scholarly journals Prediction of amphipathic helix – membrane interactions with Rosetta

2020 ◽  
Author(s):  
Alican Gulsevin ◽  
Jens Meiler
Keyword(s):  
Membrane Proteins ◽  
Md Simulations ◽  
Integral Membrane Proteins ◽  
Grid Search ◽  
Amphipathic Helix ◽  
Computational Tool ◽  
Amphipathic Helices ◽  
Peripheral Membrane Proteins ◽  
Naturally Occurring ◽  
Correlation Constant

AbstractAmphipathic helices have hydrophobic and hydrophilic/charged residues situated on opposite faces of the helix. They can anchor peripheral membrane proteins to the membrane, be attached to integral membrane proteins, or exist as independent peptides. Despite the widespread presence of membrane-interacting amphipathic helices, there is no computational tool within Rosetta to model their interactions with membranes. In order to address this need, we developed the AmphiScan protocol with PyRosetta, which runs a grid search to find the most favorable position of an amphipathic helix with respect to the membrane. The performance of the algorithm was tested in benchmarks with six engineered and 44 naturally occurring amphipathic helices using membrane coordinates from the OPM and PDBTM databases, OREMPRO server, and MD simulations as reference. The AmphiScan protocol predicted the coordinates of amphipathic helices within less than 3Å of the reference structures and identified membrane-embedded residues with a Matthews Correlation Constant (MCC) up to 0.61. Overall, AmphiScan stands as fast, accurate, and highly-customizable protocol that can be pipelined with other Rosetta and Python applications.

scholarly journals Lysine biosynthesis in Saccharomyces. Conversion of α-aminoadipate into α-aminoadipic δ-semialdehyde

1971 ◽  
Vol 125 (3) ◽  
pp. 743-749 ◽  
Author(s):  
Asru K. Sinha ◽  
J. K. Bhattacharjee
Keyword(s):  
Amino Acid ◽  
Lysine Biosynthesis ◽  
Second Step ◽  
Cell Free Extract ◽  
Experimental Conditions ◽  
Step Process ◽  
The Third ◽  
A Cell

The reduction of α-aminoadipate to α-aminoadipic δ-semialdehyde by a cell-free extract of Saccharomyces is shown to be a three-step process. First the amino acid reacts with ATP to form an adenylyl derivative. Then the adenylyl derivative of α-aminoadipate is reduced in the presence of NADPH. In the third step the reduced adenylyl derivative of the amino acid is cleaved to form α-aminoadipic δ-semialdehyde. The presence of Mg2+is necessary for the first and second steps. The third step does not need any cofactors. The product of the first step was isolated by chromatography after incubating the cell-free extract of Saccharomyces with α-aminoadipate, ATP and Mg2+. The isolated product was identified as an adenylyl derivative of α-aminoadipate and could be converted into α-aminoadipic δ-semialdehyde under the stated experimental conditions. The product of the second step was too unstable to be identified.

scholarly journals How the Use of ICT can Contribute to a Misleading Picture of Conditions – A Five-Step Process

10.28945/2322 ◽  
2015 ◽  
Vol 10 ◽  
pp. 193-215
Author(s):  
Stefan Holgersson
Keyword(s):  
Decision Making ◽  
Impression Management ◽  
Management Strategies ◽  
Holistic Approach ◽  
Second Step ◽  
Step Process ◽  
Theoretical Contribution ◽  
The Third ◽  
Fourth Step

This paper contributes to the limited research on roles ICT can play in impression-management strategies and is based on case studies done in the Swedish Police. It also gives a theoretical contribution by adopting a holistic approach to explain how ICT can contribute to giving a misleading picture of conditions. Output generated by ICT has nowadays a central role in follow-up activities and decision-making. Even if this type of output, often in colourful, presentable, graphical arrangements, gives the impression of being accurate and reliable there is a risk of defective data quality. The phenomena can be described as a process divided into five steps. The first step is about how the data is generated and/or collected. The second step is linked to how the data is registered. The third step is about the output generated from the ICT-systems. The fourth step is how the output of ICT is selected for presentation. The fifth step concerns how output generated by ICT is interpreted. This paper shows that ICT can easily be used in impression-management strategies. For example, that personnel take shortcuts to affect the statistics rather than applying methods that may give the desired effects.

scholarly journals Prediction of amphipathic helix—Membrane interactions with Rosetta

2021 ◽  
Vol 17 (3) ◽  
pp. e1008818
Author(s):  
Alican Gulsevin ◽  
Jens Meiler
Keyword(s):  
Membrane Proteins ◽  
Md Simulations ◽  
Integral Membrane Proteins ◽  
Amphipathic Helix ◽  
Score Functions ◽  
Amphipathic Helices ◽  
Peripheral Membrane Proteins ◽  
Naturally Occurring ◽  
Correlation Constant ◽  
Oppo Site

Amphipathic helices have hydrophobic and hydrophilic/charged residues situated on oppo site faces of the helix. They can anchor peripheral membrane proteins to the membrane, be attached to integral membrane proteins, or exist as independent peptides. Despite the widespread presence of membrane-interacting amphipathic helices, there is no computational tool within Rosetta to model their interactions with membranes. In order to address this need, we developed the AmphiScan protocol with PyRosetta, which runs a grid search to find the most favorable position of an amphipathic helix with respect to the membrane. The performance of the algorithm was tested in benchmarks with the RosettaMembrane, ref2015_memb, and franklin2019 score functions on six engineered and 44 naturally-occurring amphipathic helices using membrane coordinates from the OPM and PDBTM databases, OREMPRO server, and MD simulations for comparison. The AmphiScan protocol predicted the coordinates of amphipathic helices within less than 3Å of the reference structures and identified membrane-embedded residues with a Matthews Correlation Constant (MCC) of up to 0.57. Overall, AmphiScan stands as fast, accurate, and highly-customizable protocol that can be pipelined with other Rosetta and Python applications.

Image Analysis of Intramembrane Particles in Freeze-Fractured Biomembranes Using Computer Simulation Techniques

1975 ◽  
Vol 33 ◽  
pp. 214-215
Author(s):  
D.J. Benefiel ◽  
R.S. Weinstein
Keyword(s):  
Membrane Proteins ◽  
Freeze Fracture ◽  
Integral Membrane Proteins ◽  
Systematic Evaluation ◽  
Intramembrane Particles ◽  
Modeling Methods ◽  
Simulation Techniques ◽  
Freeze Fracture Electron Microscopy ◽  
Fracture Electron ◽  
Computer Simulation Techniques

Intramembrane particles (IMP or MAP) are components of most biomembranes. They are visualized by freeze-fracture electron microscopy, and they probably represent replicas of integral membrane proteins. The presence of MAP in biomembranes has been extensively investigated but their detailed ultrastructure has been largely ignored. In this study, we have attempted to lay groundwork for a systematic evaluation of MAP ultrastructure. Using mathematical modeling methods, we have simulated the electron optical appearances of idealized globular proteins as they might be expected to appear in replicas under defined conditions. By comparing these images with the apearances of MAPs in replicas, we have attempted to evaluate dimensional and shape distortions that may be introduced by the freeze-fracture technique and further to deduce the actual shapes of integral membrane proteins from their freezefracture images.

Users behaviors: The Heritage of Digital World

2014 ◽  
Vol 13 (7) ◽  
pp. 4675-4682
Author(s):  
Atefeh Danesh Moghadam ◽  
Alireza Alagha
Keyword(s):  
Technology Development ◽  
Second Step ◽  
Information Communication ◽  
The Third ◽  
Digital World ◽  
New Concepts ◽  
Emerging Patterns ◽  
History Of ◽  
Fourth Step ◽  
Communication And Technology

In the advent of information era, not only digital world is going to expand its territories, it is going to penetrate into the traditional notions about the meaning of the words and also valorize new concepts. According to Oxford Dictionary, the word heritage is defined: The history, tradition and qualities that a country or society has had for many years and that are considered an important part of its character. In order to present how emerging patterns, as the consequences of technology development, are going to be considered as the new concept of heritage, we follow four steps. In the first step, we present the convergence of Information, Communication and Technology (ICT) and a concise history of its convergence. In the second step, we argue how convergence has culminated in emerging patterns and also has made changes in digital world. In the third step, the importance of users behaviors and its mining is surveyed. Finally, in the fourth step; we illustrate User Generated Contents (UGC) as the most prominent users behaviors in digital world.

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