Protein Analysis FAQ

• • How to Predict a Peptide's Response Given Its Sequence?

  To predict a peptide's response, you can follow a systematic approach that includes sequence analysis, structure prediction, function prediction, experimental validation, machine learning and data mining, and literature search. The following details each step and its specific methods:   Sequence Analysis 1. Analysis of Basic Physicochemical Properties (1) Amino Acid Composition: Analyzing the amino acid composition helps understand its hydrophilicity or hydrophobicity. For example, peptides rich in hy......

• • Why Should Proteins Be Boiled Before SDS-PAGE Electrophoresis?

  SDS-PAGE (Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis) is a commonly used technique for protein separation. The reasons for boiling proteins before SDS-PAGE can be explained as follows:   1. Protein Denaturation Heat and SDS work together to disrupt the three-dimensional structure of the protein, converting it into a linear form. This eliminates interactions between proteins, ensuring their migration during electrophoresis is not affected by their original conformation.   2. Binding of S......

• • What Are the Differences Between Solid-Phase and Liquid-Phase Peptide Synthesis?

  Peptide synthesis refers to the chemical process of creating peptide chains. It is typically performed using solid-phase synthesis or liquid-phase synthesis. There are significant differences between these two methods, as outlined below:   Synthesis Strategy 1. Solid-Phase Synthesis Involves fixing the first amino acid on a solid support (usually resin) and progressively attaching other amino acids to form the peptide chain. After each addition, unreacted materials and by-products are washed away befo......

• • What Are the Specific Steps for DSS Protein Crosslinking?

  "DSS" (Disuccinimidyl Suberate) is a common chemical crosslinker primarily used to study and stabilize protein-protein interactions. DSS is activated as an NHS ester at room temperature and reacts with amino groups in proteins to form covalent bonds. The specific steps for DSS protein crosslinking may vary depending on your experimental needs and conditions. Below is a general procedure that may help:   1. Protein Preparation Prepare the sample containing the target proteins. If the proteins are intra......

• • Can Data Points Be Removed If R² of the Standard Curve Is Below 0.99?

  In scientific experiments, the quality of the standard curve is an important indicator for evaluating the accuracy and reliability of experimental results. If the R² value of a standard curve is below 0.99, it suggests that the correlation between the data and the fitted model may not be strong enough. Removing data points to improve the R² value should be approached cautiously, with the following considerations:   Impact of Removing Data Points Removing data points to improve the R² value can sometim......

• • How to Determine the Molecular Weight and Amino Acid Residues of a Protein? Is Experimental Detection Necessary?

  To determine the molecular weight and number of amino acid residues of a protein, there are several approaches and methods: querying public databases, using tools, and experimental detection.   Using Bioinformatics Tools and Databases 1. Database Search If the protein sequence is known, you can search for its molecular weight and amino acid sequence information in public protein databases, such as UniProt, NCBI's Protein Database, and PDB (Protein Data Bank). These databases typically list known prote......

• • Why Do Western Blot Bands Appear Darker at the Edges and Lighter in the Center?

  In Western Blot (WB) analysis, bands that are darker at the edges and lighter in the center are often due to sample overloading. When the amount of protein loaded exceeds the gel's capacity, proteins may not migrate evenly during electrophoresis, especially in the central region of the gel. This results in faster or further migration at the edges, making the center of the band appear lighter.   To address this issue, reduce the amount of protein loaded onto the gel, ensuring appropriate concentration ......

• • Does Storing Samples at -20°C for 3 Months Affect Detection Results?

  For most biological and chemical samples, storage at -20°C for up to three months generally does not significantly impact the detection results. However, the specific effects depend on the sample type and detection method. Biological samples such as DNA, RNA, and proteins can typically be stored at -20°C for extended periods without affecting subsequent molecular biology tests like PCR, Western blotting, or ELISA. However, repeated freeze-thaw cycles may damage these molecules, so it is best to avoid ......

• • What Is the Function of Histone Acetylation, and What Role Does HAT Play in This Process?

  Histone acetylation is an epigenetic modification that plays a crucial role in regulating gene expression and DNA repair. In this process, specific enzymes transfer acetyl groups (provided by acetyl-CoA) to lysine residues on histones, thereby influencing chromatin structure and function.   Functions of Histone Acetylation 1. Chromatin Relaxation The addition of acetyl groups to histones reduces their positive charge, weakening the interaction with negatively charged DNA. This results in a more relaxe......

• • What Are the Differences Between SDS and Non-SDS Systems in Protein Gel Electrophoresis?

  When performing protein gel electrophoresis, the inclusion or exclusion of SDS (sodium dodecyl sulfate) leads to distinct differences in the following aspects:   Sample Preparation 1. With SDS Adding SDS during sample preparation imparts a uniform negative charge to protein molecules and linearizes them by disrupting their secondary and tertiary structures.   2. Without SDS Omitting SDS means proteins retain their native charges and conformations during sample preparation.   Gel Preparation 1. With SD......