Multiple Protein Alignment
Multiple Protein Alignment - Related Videos
04:47
Nuclear Magnetic Resonance Spectroscopy to Identify Multiple Phosphorylations in Proteins
0 Views •
2025
This video demonstrates the use of nuclear magnetic resonance spectroscopy (NMR) techniques to identify multiple phosphorylations in a protein. The phosphorylation of a protein at specific amino acid causes the deshielding of the neighboring amide hydrogen, which generates the spectral difference.
06:32
Reverse Phase Protein Arrays Based Protein Expression Analysis: A Procedure for Simultaneous Quantification of Expression of Multiple Proteins from Cell Lysate
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2023
This video demonstrates the methodology for performing Reverse Phase Protein Arrays (RPPA) to study protein expression patterns from cell lysate. In RPPA, the lysate containing a mixture of proteins is printed on nitrocellulose slides and proteins of interest are analyzed using fluorescently labeled antibodies.
12:47
Nuclear Magnetic Resonance Spectroscopy for the Identification of Multiple Phosphorylations of Intrinsically Disordered Proteins
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Cited by 25 •
2016
We describe here a method to identify multiple phosphorylations of an intrinsically disordered protein by Nuclear Magnetic Resonance Spectroscopy (NMR), using Tau protein as a case study. Recombinant Tau is isotopically enriched and modified in vitro by a kinase prior to data acquisition and analysis.
11:36
Assembly, Loading, and Alignment of an Analytical Ultracentrifuge Sample Cell
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Cited by 21 •
2009
The analytical ultracentrifuge (AUC) sample cell holds sample and reference buffer and during experiments and is exposed to high vacuum and rotor speeds up to 60,000 rpm. This video will demonstrate the rigorous attention to detail necessary for assembly, loading and alignment of this very important component of an AUC experiment.
09:29
Isolation of Intermediate Filament Proteins from Multiple Mouse Tissues to Study Aging-associated Post-translational Modifications
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Cited by 5 •
2017
In this method, we present biochemical procedures for rapid and efficient isolation of intermediate filament (IF) proteins from multiple mouse tissues. Isolated IFs can be used to study changes in post-translational modifications by mass spectrometry and other biochemical assays.
FAQs
Scoring choices determine which alignment is favored. A substitution matrix assigns relative scores to amino acid matches and substitutions, while gap penalties regulate the cost of introducing gaps. Changing these settings can therefore alter how similarities, substitutions, and gaps are arranged, affecting which regions appear conserved and how confidently relationships are interpreted.
A guide tree sets the order for progressive alignment. Sequences judged most similar are aligned first, and their combined alignment is then extended as additional sequences join. A later refinement step can adjust the composite arrangement. This strategy uses estimated sequence similarity to organize the analysis before refinement, so the guide tree influences how related sequences are compared.
Conserved positions across aligned proteins can highlight motifs or catalytic residues, whereas variable positions show where sequences differ. In genetics, this contrast helps researchers assess homology and consider whether a mutation could affect protein structure or function. The alignment therefore links sequence variation with testable functional questions.
A typical analysis starts by collecting at least three protein sequences and comparing their similarity. The sequences are scored for matches, substitutions, and gaps, then a guide tree orders progressive alignment. Researchers can subsequently refine the combined alignment to improve the arrangement of corresponding positions across sequences.
Multiple Protein Alignment is useful when researchers need to assess homology among proteins, examine functional relationships, or identify sequence features shared across related proteins. It can also support evolutionary tree construction and evaluation of how mutations may influence structural or functional properties. These uses connect sequence patterns with biological interpretation.
In genetics, the alignment provides a way to compare protein-level consequences of sequence variation across sequences. Conserved motifs and catalytic residues can guide attention toward regions with potential functional importance, while variable regions help distinguish evolutionary differences. Results can inform comparative genomics and help researchers design follow-up experimental work focused on protein function.