Driven by increasing interests in sequencing proteins, several single molecule methods (such as the measurement of electron tunneling currents through each amino acid) have been recently proposed and demonstrated in experiment. While promising, they are still in early stages and challenges such as the lack of protein stretching and large thermal fluctuations of amino acids remain to be solved. Here, we show that a patterned two dimensional (2D) in-plane heterostructure comprising both graphene and hexagonal boron nitride (hBN) domains can be utilized to stretch the intrinsically disordered Aβ42 protein because of the chemical potential difference between the graphene and hBN surfaces. Additionally, thanks to the physisorption of the flexible Aβ42 protein on the 2D surface, thermal fluctuations of amino acids are substantially reduced. Therefore, this stretched protein conformation with amino acids adsorbed on the 2D surface may facilitate protein sequencing using the high resolution atomic force microscopy (AFM) or scanning tunneling microscope (STM), with improved signal-to-noise ratios. We further show that the 2D-heterostructure-based protein electrophoresis can help detect the phosphorylation in a single protein molecule. We expect that the patterned 2D heterstructure could serve as a new versatile platform for various single-protein analyses.