nucleic: lec 8

Aligning protein structures to highlight similarities and differences by placing them on top of each other.

A measurement used to quantify the closeness of fit between two superimposed protein structures. Lower RMSD values indicate greater similarity.

Proteins with similar structures and sequences, often suggesting evolutionary relatedness.

A powerful software tool for analyzing and visualizing protein structures, particularly effective for aligning homologous structures.

A software tool for aligning protein structures regardless of their sequence similarity.

A way to represent protein structure by showing the distances between all pairs of amino acids. This allows comparison of structural similarity without superposition.

Aligning protein structures to find similarities and differences. This involves placing structures on top of each other to visually compare them.

Distance matrices are used to analyze protein structures because they contain all the information needed to reconstruct the protein's 3D shape, except for its chirality (left- or right-handedness).

Distance matrices are convenient for comparing protein structures because they are independent of orientation and focus on the overall pattern of distances between amino acids, making them easier to analyze.

DALI is a tool that identifies structural similarities between proteins by comparing their distance matrices. It assigns a Z-score to indicate the significance of the similarity.

The Z-score from DALI indicates how likely the observed structural similarity is due to chance. A high Z-score suggests strong homology, while a low Z-score implies weak or coincidental similarity.

The "Length Aligned" value in a DALI analysis indicates whether the similarity between proteins extends across their entire length or is limited to a specific sub-domain.

A high Z-score (above 10) in DALI analysis suggests a strong structural similarity, indicating that the two proteins are likely homologous.

A low Z-score (below 2) suggests a weak or coincidental structural similarity. This means the proteins are likely not homologous.

A Z-score between 2-5 indicates a weak structural similarity. While the proteins may share some similarities, they are likely not closely related. This might indicate a similar function or a shared structural motif.

Root Mean Square Deviation (RMSD) quantifies how well two protein structures align (superimpose) on top of each other. A lower RMSD value indicates that the structures are more similar.

Z-score, calculated by DALI, helps you interpret the significance of observed structural similarities between proteins. It tells you whether two proteins are truly related or if their similarity is simply a coincidence.

Small molecules or cofactors that bind to proteins can provide clues about their function. Analyzing the binding sites and types of ligands can give insights into how the protein functions.

By aligning (superposing) structures of similar proteins where ligands are known, we can predict how ligands might bind to proteins with unknown binding sites.

Glycerol and ethylene glycol are often used to preserve protein structures during freezing. These molecules can bind in the structure, but they don't usually have biological significance.

Sometimes, buffer salts like sodium and chloride ions can bind to a protein in a structure. These are not necessarily the same ions that bind in the protein's natural function.

Differences in ligand binding sites between similar proteins might indicate evolutionary changes or the use of slightly different ligands.

Amino acids that are highly similar across different species, suggesting important roles in protein structure or function.

Amino acids that can change without affecting protein function, often located in less critical positions.

ConSurf analysis helps identify regions of proteins that are important for their function and are likely to be conserved across evolution.

The number and arrangement of subunits in a protein complex.

Cryo-electron microscopy (Cryo-EM) directly observes the protein complex to determine its oligomeric state.

A tool that predicts possible oligomeric states for proteins based on their crystal structure.

Crystal contacts are interactions introduced by the crystal structure. These are often biologically irrelevant and should be distinguished from biologically critical contacts.

Always verify the predicted oligomeric state by considering sequence conservation, as PISA alone may not guarantee the biological relevance of an oligomer.

Amino acids that are very similar across different species, indicating key roles in protein function or structure. They can be found on the protein's surface (functional) or buried inside (structural).

Amino acids that have more flexibility in their sequence, often not directly involved in the protein's main function or stability. They are more tolerant to changes.

A method that uses evolutionary information to highlight regions of a protein that are important for its function. It colors a protein structure based on the conservation of its amino acids.

A high conservation score in ConSurf indicates that a region of the protein is very important for its function and is highly unlikely to change over time.

The process of figuring out the number and arrangement of subunits in a protein complex. It helps us understand how proteins interact and work together.

Sequence conservation helps confirm the biological relevance of predicted oligomeric states from crystal structures. It examines whether amino acids involved in interactions are conserved, suggesting their importance for function.