Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations in the cell or outside it. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to exterior of the cell via secretion.
Protein targeting or protein sorting is the mechanism by which a cell transports to the appropriate positions in the cell or outside of it. Both in prokaryotes and eukaryotes, newly synthesized proteins must be delivered to a specific sub-cellular location or exported from the cell for correct activity. This phenomenon is called protein targeting. Protein targeting is necessary for proteins that are destined to work outside the cytoplasm.This delivery process is carried out based on information contained in the protein itself. Correct sorting is crucial for the cell; errors can lead to diseases. In 1970, Günter Blobel conducted experiments on the translocation of proteins across membranes. He was awarded the 1999 Nobel Prize for his findings. He discovered that many proteins have a signal sequence, that is, a short amino acid sequence at one end that functions like a postal code for the target organelle.
I have tried to make a precise presentation on protein transport, targeting and sorting into organelle's other than nucleus. Hope this might help you. Comments are welcome.
Protein targeting or protein sorting is the mechanism by which a cell transports to the appropriate positions in the cell or outside of it. Both in prokaryotes and eukaryotes, newly synthesized proteins must be delivered to a specific sub-cellular location or exported from the cell for correct activity. This phenomenon is called protein targeting. Protein targeting is necessary for proteins that are destined to work outside the cytoplasm.This delivery process is carried out based on information contained in the protein itself. Correct sorting is crucial for the cell; errors can lead to diseases. In 1970, Günter Blobel conducted experiments on the translocation of proteins across membranes. He was awarded the 1999 Nobel Prize for his findings. He discovered that many proteins have a signal sequence, that is, a short amino acid sequence at one end that functions like a postal code for the target organelle.
I have tried to make a precise presentation on protein transport, targeting and sorting into organelle's other than nucleus. Hope this might help you. Comments are welcome.
Each cell in the human contains all the genetic material for the growth and development of a human
Some of these genes will be need to be expressed all the time
These are the genes that are involved in of vital biochemical processes such as respiration
Other genes are not expressed all the time
They are switched on an off at need
SOS repair
a system that repairs severely damaged bases in DNA by base excision and replacement, even if there is no template to guide base selection. This process is a last resort for repair and is often the cause of mutations.
CBCS 4TH SEM ,
CHARGING, STRUCTURE AND FUNCTION OF tRNA,
AMINOACYL RNA SYNTHETASE(ASR) PROOFREADING AND EDITING
https://www.youtube.com/watch?v=YzOVMWYLiCE
Details of cytoskeleton element-microtubule. The Microtubule associated protein-type and function, Treadmilling and dynamic instability, Structure of cilia and flagella
A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle.
More than half of all proteins interact with membranes.
The delivery of newly synthesized protein to their proper cellular destination, usually referred to as protein targeting or sorting.
The mode of protein transport depends chiefly on the location in the cell cytoplasm of the polysomes involved in protein synthesis.
There are two modes of protein sorting:-
1) Co - translational Transportation.
2) Post - translational Transportation.
Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations in the cell or outside it. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to exterior of the cell via secretion.
Each cell in the human contains all the genetic material for the growth and development of a human
Some of these genes will be need to be expressed all the time
These are the genes that are involved in of vital biochemical processes such as respiration
Other genes are not expressed all the time
They are switched on an off at need
SOS repair
a system that repairs severely damaged bases in DNA by base excision and replacement, even if there is no template to guide base selection. This process is a last resort for repair and is often the cause of mutations.
CBCS 4TH SEM ,
CHARGING, STRUCTURE AND FUNCTION OF tRNA,
AMINOACYL RNA SYNTHETASE(ASR) PROOFREADING AND EDITING
https://www.youtube.com/watch?v=YzOVMWYLiCE
Details of cytoskeleton element-microtubule. The Microtubule associated protein-type and function, Treadmilling and dynamic instability, Structure of cilia and flagella
A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle.
More than half of all proteins interact with membranes.
The delivery of newly synthesized protein to their proper cellular destination, usually referred to as protein targeting or sorting.
The mode of protein transport depends chiefly on the location in the cell cytoplasm of the polysomes involved in protein synthesis.
There are two modes of protein sorting:-
1) Co - translational Transportation.
2) Post - translational Transportation.
Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations in the cell or outside it. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, plasma membrane, or to exterior of the cell via secretion.
Intracellular Traffic and Sorting of ProteinsASHIKH SEETHY
Describes intra-cellular trafficking of proteins, protein sorting, clinical aspects of protein targeting, and vesicle transport.
Download and view in slide show mode for better viewing.
Protein targeting or protein sorting is the mechanism by which a cell transports proteins to the appropriate positions in the cell or outside of it.
Protein transport from ER to Golgi complex
Protein transport into Mitochondria
Transport of protein-protein translocators in mitochondrial membrane
Membrane protein of mitochondria
Component required for protein transport
This presentation covers a general introduction to expression vector, its components, types, and its application. Then it covers some of the expression system with examples.
Proteins destined for secretion, integration in the plasma membrane, or inclusion in lysosomes generally share pathway that begins in the endoplasmic reticulum. Proteins destined for mitochondria, chloroplasts, or the nucleus use three separate mechanisms. And proteins destined for the cytosol simply remain where they are synthesized.
Proteins destined for secretion, integration in the plasma membrane, or inclusion in lysosomes generally share pathway that begins in the endoplasmic reticulum. Proteins destined for mitochondria, chloroplasts, or the nucleus use three separate mechanisms. And proteins destined for the cytosol simply remain where they are synthesized.
The term isolation refers to the separation of a strain from a natural, mixed population of living microbes, as present in the environment. It becomes necessary to maintain the viability and purity of the microorganism by keeping the pure culture free from contamination.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Nucleophilic Addition of carbonyl compounds.pptxSSR02
Nucleophilic addition is the most important reaction of carbonyls. Not just aldehydes and ketones, but also carboxylic acid derivatives in general.
Carbonyls undergo addition reactions with a large range of nucleophiles.
Comparing the relative basicity of the nucleophile and the product is extremely helpful in determining how reversible the addition reaction is. Reactions with Grignards and hydrides are irreversible. Reactions with weak bases like halides and carboxylates generally don’t happen.
Electronic effects (inductive effects, electron donation) have a large impact on reactivity.
Large groups adjacent to the carbonyl will slow the rate of reaction.
Neutral nucleophiles can also add to carbonyls, although their additions are generally slower and more reversible. Acid catalysis is sometimes employed to increase the rate of addition.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
2. 2 Protein Targeting pathways
Protein synthesis always
begins on free ribosomes
In cytoplasm
1) Post -translational: proteins
of plastids, mitochondria,
peroxisomes and nuclei
2) Endomembrane system
proteins are imported
co-translationally
3. 2 pathways for Protein Targeting
1) Post -translational
2) Co-translational: Endomembrane system proteins are
imported co-translationally
inserted in RER
as they are made
transported to
final destination
in vesicles
4. SIGNAL HYPOTHESIS
Protein synthesis begins on free ribosomes in cytoplasm
endomembrane proteins have "signal sequence"that
directs them to RER
“attached” ribosomes are
tethered to RER by
the signal sequence
5. SIGNAL HYPOTHESIS
• Protein synthesis begins on free ribosomes in cytoplasm
• Endomembrane proteins have "signal sequence"that
directs them to RER
• SRP (Signal Recognition Peptide) binds signal sequence
when it pops out of ribosome & swaps GDP for GTP
6. SIGNAL HYPOTHESIS
SRP stops protein synthesis until it binds “docking
protein”(SRP receptor) in RER
Ribosome binds Translocon & secretes protein through it
as it is made
BiP (a chaperone) helps the protein fold in the lumen
7. Subsequent events
Simplest case:
1) signal is cleaved within lumen by signal peptidase
2) BiP helps protein fold correctly
3) protein is soluble inside lumen
9. proteins embedded in membranes
protein has a stop-transfer sequence
too hydrophobic to enter aqueous lumen
10. proteins embedded in membranes
protein has a stop-transfer sequence
too hydrophobic to enter lumen
therefore gets stuck in membrane
ribosome releases translocon, finishes job in cytoplasm
13. Sorting proteins made on RER
Simplest case: no sorting
• proteins in RER lumen
are secreted
Cytoplasm
Endoplasmic reticulum
Golgi Apparatus
Plasma Membrane
Secretory
vesicles
14. Sorting proteins made on RER
Simplest case: no sorting
• proteins in RER lumen
are secreted
• embedded proteins
go to plasma membrane
Cytoplasm
Endoplasmic reticulum
Golgi Apparatus
Plasma Membrane
Secretory
vesicles
16. Sorting proteins made on RER
Redirection requires extra information:
1) specific motif
2) receptors
17. Sorting proteins made on RER
ER lumen proteins have KDEL (Lys-Asp-Glu-Leu) motif
Receptor in Golgi binds & returns these proteins
ER membrane proteins
have KKXX motif Cytoplasm
Endoplasmic reticulum
Golgi Apparatus
18. Sorting proteins made on RER
Golgi membrane proteins
• cis- or medial- golgi proteins are
marked by sequences in the
membrane-spanning domain
• trans-golgi proteins have a
tyrosine-rich sequence in their
cytoplasmic C-terminus
Cytoplasm
Endoplasmic reticulum
cis- Golgi
trans- Golgi
medial- Golgi
19. Sorting proteins made on RER
Plant vacuolar proteins are zymogens (proenzymes)
Cytoplasm
Endoplasmic reticulum
Golgi Apparatus
Vacuole
signal
signal
VTS
VTS
Barley aleurain
Barley lectin
mature protein
mature protein
20. Sorting proteins made on RER
Plant vacuolar proteins are zymogens (proenzymes),
cleaved to mature form on arrival
• targeting motif may be
at either end of protein
Cytoplasm
Endoplasmic reticulum
Golgi Apparatus
Vacuole
signal
signal
VTS
VTS
Barley aleurain
Barley lectin
mature protein
mature protein
21. Sorting proteins made on RER
lysosomal proteins are targeted by
mannose 6-phosphate
M 6-P receptors in trans-Golgi
direct protein to lysosomes (via
endosomes)
M 6-P is added in Golgi by enzyme
that recognizes lysosomal motif
22. Glycosylation within ER
All endomembrane proteins are highly glycosylated on
lumenal domains.
Glycosylation starts in the ER, continues in the Golgi
23. Glycosylation within ER
All endomembrane proteins are highly glycosylated on
lumenal domains.
Glycosylation starts in ER, continues in Golgi
makes proteins more hydrophilic
essential for proper function
tunicamycin poisons cells
Glycosylation mutants are even sicker
24. Glycosylation in RER
remove 2 glucose & bind to chaperone
If good, remove gluc 3 & send to Golgi
If bad, GT adds glucose
& try again
Eventually, send bad
proteins to cytosol
& eat them
27. Post-translational
protein targeting
Key features
1) imported after
synthesis
2) targeting
information is
motifs in protein
a) which organelle
b) site in organelle
3) Receptors guide
it to correct site
4) no vesicles!
28. Protein targeting in Post-translational pathway
SKL (ser/lys/leu) at C terminus targets most peroxisomal
matrix proteins = PTS1
In humans 3 are targeted by 9 aa at N terminus = PTS2
Defective PTS2 receptor causes Rhizomelic
chondrodysplasia punctata
N CSKL
N CPTS2
29. Targeting peroxisomal proteins
• Bind receptor in cytoplasm
• Dock with peroxisomal receptors
• Import
protein w/o
unfolding it!
• Recycle
receptors
30. Peroxisomal Membrane Synthesis
Most peroxisomes arise by fission
can arise de novo!
Mechanism is poorly understood/ may involve ER!
Only need PEX 3 & PEX 16 to import pex membrane prot
31. Protein import into nuclei
nuclear proteins are targeted by internal motifs
necessary & sufficient to target cytoplasmic proteins
to nucleus
32. Protein import into nuclei
nuclear proteins are targeted by internal motifs
as in golgi, are not specific
shapes cf sequences
Receptors bind objects of the right shape!
33. Protein import into nuclei
3 types of NLS (nuclear localization sequence)
1) basic residues in DNA-binding region
+ + +
LZ
34. Protein import into nuclei
3 types of NLS (nuclear localization sequence)
1) basic residues in DNA-binding region
2) SV-40 KKKRK
KKKRK
+ + +
LZ
35. Protein import into nuclei
3 types of NLS (nuclear localization sequence)
1) basic residues in DNA-binding region
2) SV-40 KKKRK
3) bi-partite: 2-4 basic aa,10-20 aa spacer, 2-4 basic aa
KKKRK
+ + +
LZ
+ ++ +
36. Protein import into nuclei
1) importin−α binds NLS
importin−β binds complex
2) escort to nuclear pores
•Pores decide who can
enter/exit nucleus
37. Protein import into nuclei
1) importin−α binds NLS, importin−β binds complex
2) escort to nuclear pores
3) transporter changes shape, lets complex enter
4) nuclear Ran-GTP dissociates complex
5) Ran-GTP returns β−importin to cytoplasm, becomes
Ran-GDP. GTP -> GDP = nuclear import energy source
6) Exportins return α−importin & other cytoplasmic prot