Question

Problem 4 (15 points): This is a take home group work that will require you to work with protein data bank and possibly proteopedia to collect information about various proteins. Please complete this and bring a hard copy of this to start of class on Tuesday, June 4th Protein data bank ID Protein Role of Location of protein First 5 amino acids of Does it have a signal peptide? Does it have a disulfide bond? One example of modified amino acid Your protein description of 3° structure code mature protein (3 letter) 1HGV 3CQX 1H4W 4PYP 2BJX 1QLZ 1AKM

Answer 1

Protein data bank ID code	Protein	Role of protein	Location of protein	First 5 amino acids of mature protein (3 letter)	Does it have a signal peptide?	Does it have a disulfide bond?	One example of modified amino acid	Your description of 3' structure
1HGV	Filamentous Bacteriophage PH75	PH75 INOVIRUS MAJOR COAT PROTEIN p8 in Thermus phage PH75 strain	Outer coat of virus	MDFNP- Met, Asp, Phe, Asn, Pro	The p8 protein is synthesized without a leader sequence	No disulphide bonds seen on Pymol view (click on 3D view, then download files, then PDB format. The file can be opened in Pymol. Click on ‘S’, then disulfide bond)		It looks like an alpha helix turned around an axis
3CQX	Chaperone Complex (HEAT SHOCK COGNATE 71 KDA PROTEIN)	Cochaperones are essential for Hsp70- and Hsc70-mediated folding of proteins and include nucleotide-exchange factors (NEFs) that assist protein folding by accelerating ADP-ATP exchange on Hsp70.	MUS MUSCULUS (mouse)	GLY ALA MET GLY SER		Disulfide bonds were not seen in Pymol view		It looks like 2 pillars connected by a bridge
1H4W	human trypsin IV	human trypsin IV, is likely to be involved in the pathomechanism of these disease like severe neurodegradative brain diseases, like Alzheimer.	Human brain	ILE VAL GLY GLY TYR		Yes
4PYP	human glucose transporter GLUT1	The glucose transporter GLUT1 catalyses facilitative diffusion of glucose into erythrocytes and is responsible for glucose supply to the brain and other organs.	Homo sapiens	MEPSS (MET GLU PRO SER SER)		No disulfide bonds		It looks like several alpha helix pillars decorated with filia like structures at both ends.
2BJX	PROTEIN DISULFIDE ISOMERASE	Protein disulfide isomerase (PDI) is a multifunctional protein of the endoplasmic reticulum, which catalyzes the formation, breakage and rearrangement of disulfide bonds during protein folding.	Endoplasmic reticulum in human cell	AATTL (Ala, Ala, Thr, Thr, Leu)		No disulfide bond		A few alpha helix interconnected by strands
1QLZ	PRION Protein	It is a structural protein	Homo sapiens	GSKKR (Gly, Ser, Lys, Lys, Arg)		Yes, there is disulfide bond (can view as line or stick or sphere)		A few alpha helix interconnected by strands
1AKM	ORNITHINE TRANSCARBAMYLASE FROM ESCHERICHIA COLI	It acts as transferase enzyme	E.coli	SGFYH (Ser, Gly, Phe,Tyr,His)		No.		It is very complicated with several alpha helix