A New Structural Model of Apolipoprotein B100 Based on Computational Modeling and Cross Linking.

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Apolipoprotein B-100 (apoB-100) is vital in lipid transport and cardiovascular disease development.
• Limited structural information exists for apoB-100, hindering functional understanding.

Purpose of the Study:

• To determine the three-dimensional structure of apoB-100.
• To elucidate the functional mechanisms of apoB-100 in lipoprotein particle dynamics and receptor binding.

Main Methods:

• A novel 'divide and conquer' computational approach using PSIPRED software.
• Domain modeling via I-TASSER, DEMO, RoseTTAFold, Phyre2, and MODELLER.
• Experimental validation using disuccinimidyl sulfoxide (DSSO) mass spectrometry and disulfide bond analysis.

Main Results:

• A high-resolution structural model of apoB-100 was generated, integrating computational and experimental data.
• 87.5% of 65 unique DSSO cross-links fell within a 26 Å threshold, validating the model.
• Disulfide bond positions were confirmed within a 5.6 Å constraint.
• Computational models of VLDL and LDL revealed dynamics during particle size transitions.

Conclusions:

• The study presents the first comprehensive structural model of apoB-100, integrating multiple computational and experimental techniques.
• The validated model offers new insights into apoB-100's role in lipid transport, cardiovascular disease, and receptor interactions.
• Understanding apoB-100 structure and dynamics is critical for developing targeted therapies for cardiovascular diseases.