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ESM3 is a pre-trained model that we used to generate functional proteins. We wanted to know if it had enough biological accuracy to do this task.
Fluorescence is a phenomenon where certain materials emit light after absorbing light or other electromagnetic radiation. It is a type of luminescence and is commonly observed in fluorescent minerals, dyes, and biological molecules. In this context, we are discussing the use of fluorescence in a specific application.
GFP chromophore cofactors substrates
Proteins in the GFP family are responsible for the bright colors seen in jellyfish and coral. These proteins have a unique ability to create a fluorescent chromophore without needing any additional molecules. This is different from other fluorescent proteins that require cofactors or substrates to create their chromophore.
GFP sequence genomes organisms label molecules cellular structures processes foundational toolkit biosciences
GFP protein engineering prospecting
The GFP family refers to a group of proteins that have been extensively studied and modified over the years. Despite these efforts, most of the useful variants have been found in nature rather than created through engineering.
Protein engineering is the process of modifying proteins to improve their properties or create new ones. This can involve changing the amino acid sequence or adding new functional groups.
Prospecting refers to the process of searching for useful proteins in nature. This can involve screening organisms for specific properties or using computational methods to predict protein structures and functions.
Rational design and machine learning-assisted high-throughput screening have yielded GFP sequences with improved properties, such as higher brightness or stability, or differently colored variants, that incorporated small numbers of mutations (typically 5 to 15, out of the total 238 amino acid coding sequence) from the originating sequence.
In simpler terms, scientists have used a combination of rational design and machine learning to create new versions of a protein called GFP (green fluorescent protein) that have better qualities than the original. They did this by making small changes to the protein's genetic code, which resulted in new versions that are brighter, more stable, or have different colors. These changes were made using a process called high-throughput screening, which allows scientists to test many different versions of the protein at once.
mutations high throughput experimentation
In this paragraph, the author is discussing the process of introducing mutations into a system. They mention that in rare cases, scientists have been able to introduce up to 40-50 mutations using a technique called high throughput experimentation. This technique involves performing a large number of experiments in a short amount of time, allowing scientists to quickly test different mutations and see their effects on the system.
Sure, I'd be happy to help! Here's an example of how to create an Obsidian markdown internal link:
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Laparoscopic Cholecystectomy Risks
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GFP fluorescence sequence identity
In this paragraph, the author is discussing the process of creating a new type of fluorescent protein called GFP. They mention that this process would require a deep understanding of the complex biochemistry and physics involved in how GFP fluoresces.
GFPs chromophore autocatalytic process amino acids
In this paragraph, GFPs refer to green fluorescent proteins, which are commonly used in biotechnology and medical research. The chromophore is a part of the protein that gives it its fluorescent properties. The autocatalytic process is a chemical reaction that occurs within the protein and helps to form the chromophore. Finally, amino acids are the building blocks of proteins and play a crucial role in the formation of the chromophore.
The unique structure of GFP, a kinked central alpha helix surrounded by an eleven stranded beta barrel
The unique structure of GFP, a kinked central alpha helix surrounded by an eleven stranded beta barrel, is what gives it its fluorescent properties. GFP stands for Green Fluorescent Protein, which is a protein that emits green light when exposed to ultraviolet or blue light. The alpha helix is a type of secondary structure in proteins, while the beta barrel is a type of tertiary structure. The combination of these structures in GFP allows it to fluoresce, making it a useful tool in biological research.
mathpix is a tool that allows you to take a picture of a handwritten math equation and convert it into a digital format that can be easily edited and shared. This is particularly useful for students and educators who need to work with math equations on a regular basis.
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In Figure 4, we can see a visual representation of the data collected from our experiment. The graph shows the relationship between the independent variable and the dependent variable. The x-axis represents the independent variable, while the y-axis represents the dependent variable. The data points are plotted on the graph, and a trend line is drawn to show the overall pattern of the data. This graph helps us to better understand the relationship between the two variables and draw conclusions from our experiment.
Generating a new fluorescent protein with a chain of thought
ESM3 is a program that helps us understand how certain proteins work. In this case, we are using it to study a specific part of a protein called the chromophore reaction. We also need to know the structure of a part of the protein called the central alpha helix. By using ESM3, we can better understand how this protein works and potentially use that knowledge to develop new technologies or treatments.
ESM3 is a software tool that uses a chain of thought to generate design candidates. It is a helpful tool for non-experts who may not be familiar with the technical jargon. ESM3 stands for "Engineering System Modeler 3" and is a program that assists in the design process by generating potential solutions based on a set of criteria. This can be useful for those who may not have extensive knowledge in the field and need assistance in creating designs.
coli lysate is a solution that contains the remains of E. coli bacteria that have been broken open. This solution is often used in laboratories to study proteins and other molecules that are found inside the bacteria. By breaking open the bacteria, scientists can access these molecules and study them in more detail. coli lysate is an important tool in many areas of biological research, including genetics, biochemistry, and microbiology.
The top row of the photograph shows plates. These are flat, circular objects typically used for serving food.
The top row of the photograph shows plates. These are flat, circular objects typically used for serving food.
Bottom row, plate reader fluorescence quantification
GFP E. coli purple circles negative controls
In this paragraph, the author is discussing the use of positive and negative controls in an experiment involving GFP (green fluorescent protein) and E. coli (a type of bacteria). The positive controls are marked with purple circles, indicating that they are known to contain GFP. The negative controls, on the other hand, do not contain any GFP sequence or E. coli, and are used to ensure that any results obtained are not due to contamination or other factors.
Coli are a type of bacteria commonly found in the gut of humans and animals. They are often used as an indicator of fecal contamination in water and food. In this context, the presence of Coli in water samples suggests that the water may be contaminated with fecal matter and therefore unsafe for consumption. It is important to monitor for Coli in order to prevent the spread of waterborne illnesses.
In the first experiment (left) we expressed designs with a range of sequence identities.
In the first experiment, we used designs with different levels of sequence identities. Sequence identity refers to the degree of similarity between two DNA or protein sequences. By varying the sequence identity, we were able to test the performance of our designs under different conditions.
In this paragraph, the author is discussing a specific design that is labeled B8. This design is notable because it has a low sequence identity to known fluorescent proteins. The author has highlighted B8 in a black circle at the bottom and a white circle at the top.
In this paragraph, we are discussing a specific type of design that appears in a well labeled C10. We have designated this design as esmGFP. The design is described as "bright" and is labeled with black and white circles.
esmGFP is a type of protein that exhibits fluorescence intensity similar to common GFPs. GFP stands for green fluorescent protein, which is a protein that emits green light when exposed to certain types of light. This is useful in scientific research as it allows scientists to track the location and movement of cells or molecules within cells. The "esm" in "esmGFP" stands for "extended Stokes shift," which means that the protein has a larger difference between the wavelengths of light it absorbs and emits, making it easier to distinguish from other fluorescent proteins.
Normalized fluorescence is a term used in scientific research to describe the process of adjusting the intensity of fluorescence to a standard level. This is done to ensure that the results obtained from different experiments can be compared accurately. In the context of the given paragraph, it means that the fluorescence levels of a specific set of proteins were adjusted to a standard level in experiment 2. This was likely done to compare the results of this experiment with those of other experiments.
The paragraph discusses the differences between two types of fluorescent proteins, esmGFP and tagRFP. The author notes that there are 96 mutations that distinguish esmGFP from tagRFP, and these mutations are highlighted in blue.
Cumulative density of sequence identity between fluorescent proteins across taxa
esmGFP has the level of similarity to all other FPs that is typically found when comparing sequences across orders, but within the same class.
This paragraph discusses the evolutionary distance and sequence identities of three different types of GFPs (green fluorescent proteins) found in anthozoa, a group of marine animals that includes corals and sea anemones. The GFPs are compared based on their evolutionary distance, which is measured in millions of years, and their sequence identities, which refer to the degree of similarity between their genetic sequences. The paragraph also mentions esmGFP, which is a type of GFP that has been engineered to be more stable and brighter than natural GFPs.
esmGFP is a protein that is estimated to be over 500 million years of natural evolution removed from the closest known protein. This means that it has undergone a significant amount of changes and mutations over time, resulting in a unique structure and function. Understanding the properties of esmGFP can provide insights into the evolution of proteins and their role in biological processes.
inward facing coordinating residues reaction (49)
The phrase "inward facing coordinating residues" refers to specific amino acid residues within a protein that are positioned in a way that allows them to interact with each other and facilitate a chemical reaction. This is important for the proper functioning of the protein. The term "reaction (49)" likely refers to a specific chemical reaction that is being discussed in the context of the text.
In order for a substance to be fluorescent, it must first absorb light and then emit it. This process involves the formation of a chromophore, which is a molecule that absorbs light. However, simply absorbing light is not enough for fluorescence to occur. The chromophore must also be able to emit the absorbed light in order to create the fluorescent effect.
Light emission is the process by which an object emits light. In this context, it refers to the emission of light by a chromophore, which is a molecule that absorbs and emits light. The sensitivity of light emission to the local electronic environment of the chromophore means that changes in the environment can affect the amount and properties of the light emitted. This is important in fields such as optics and photonics, where the manipulation of light is crucial for various applications.
1). GFP ESM3 chromophore reaction
In this paragraph, we are discussing the process of creating new GFP sequences. GFP stands for Green Fluorescent Protein, which is a protein that emits green light when exposed to certain types of light. ESM3 is a type of artificial intelligence model that is used to generate new protein sequences. The chromophore reaction is the process by which GFP emits light. The critical residues for this process are Thr62, Thr65, Tyr66, Gly67, Arg96, and Glu222. By using ESM3 to generate new GFP sequences, we hope to create proteins that emit light in different colors or under different conditions.
In this paragraph, the author is discussing the use of a specific experimental structure (1QY3) to understand the formation of chromophores, which are molecules that absorb and emit light. They are specifically focusing on residues 58 through 71, which have been shown to be important for the energetic favorability of chromophore formation. By using this structure as a reference, the author hopes to gain a better understanding of how chromophores are formed and how they function.
Sequence tokens Structure tokens Atomic coordinates Backbone
In this paragraph, the author is discussing the process of generating a protein structure using a set of input data. The input data includes "sequence tokens," which are essentially the building blocks of the protein, as well as "structure tokens" and "atomic coordinates" that provide additional information about the protein's shape and composition. The author also mentions the "backbone," which refers to the main chain of the protein. The process of generating the protein structure begins with a "masked array of tokens" that contains information about 229 residues, or building blocks, of the protein. The author notes that this array is "nearly completely masked," meaning that some of the information is hidden or obscured. The process of generating the protein structure involves using this masked array, along with additional information provided by the sequence tokens, structure tokens, and atomic coordinates, to create a complete picture of the protein's structure.
In this procedure, we start with a problem and generate a solution by following a chain of thoughts. Each thought is based on the previous one and leads to the next one. We continue this process until we reach a satisfactory solution.
For example, if the problem is to design a new product, we might start by thinking about the target audience and their needs. This could lead us to consider different features that would meet those needs, and then to brainstorm various designs that incorporate those features. We would continue refining our ideas until we have a final design that we are happy with.
Structure tokens are generated by the model to create a protein backbone. This is an important step in the process of creating a protein structure.
In this paragraph, the author is discussing a process where backbones are being filtered based on their atomic coordination and overall structure. The term "backbones" refers to the main structural components of a molecule or protein. The author is using a filter to select backbones that have good atomic coordination in the active site, which is the part of the molecule or protein where chemical reactions occur. The backbones also need to have a differentiated overall structure from the 1QY3 backbone, which is a specific type of backbone that is being used as a reference. Once the backbones pass through this filter, they move on to the next step in the process.
Obsidian markdown internal links are a way to link to other notes or pages within Obsidian, a note-taking app. They are created by enclosing the name of the note or page you want to link to in double brackets, like this: link. However, if the name of the note or page contains spaces, you need to replace those spaces with underscores, like this: linkwithspaces.
In the context of the original prompt, the use of obsidian markdown internal links is likely a way to organize and connect different notes or pages related to the topic being discussed. By creating these links, the author can easily navigate between different sections of their notes and keep track of related information.
In this process, we alternate between optimizing the sequence and the structure of a system. This helps us to improve the overall performance of the system by making small adjustments to both the sequence and structure.
The sequence refers to the order in which tasks or operations are performed in a system. By optimizing the sequence, we can improve the efficiency and effectiveness of the system.
The structure refers to the overall design and organization of a system. By optimizing the structure, we can improve the stability and reliability of the system.
We reject chainsof-thought that lose atomic coordination of the active site (Appendix A