5C67

Human Mesotrypsin in complex with amyloid precursor protein inhibitor variant APPI-M17G/I18F/F34V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Combinatorial protein engineering of proteolytically resistant mesotrypsin inhibitors as candidates for cancer therapy.

Cohen, I.Kayode, O.Hockla, A.Sankaran, B.Radisky, D.C.Radisky, E.S.Papo, N.

(2016) Biochem.J. 473: 1329-1341

  • DOI: 10.1042/BJ20151410

  • PubMed Abstract: 
  • Engineered protein therapeutics offer advantages, including strong target affinity, selectivity and low toxicity, but like natural proteins can be susceptible to proteolytic degradation, thereby limiting their effectiveness. A compelling therapeutic ...

    Engineered protein therapeutics offer advantages, including strong target affinity, selectivity and low toxicity, but like natural proteins can be susceptible to proteolytic degradation, thereby limiting their effectiveness. A compelling therapeutic target is mesotrypsin, a protease up-regulated with tumour progression, associated with poor prognosis, and implicated in tumour growth and progression of many cancers. However, with its unique capability for cleavage and inactivation of proteinaceous inhibitors, mesotrypsin presents a formidable challenge to the development of biological inhibitors. We used a powerful yeast display platform for directed evolution, employing a novel multi-modal library screening strategy, to engineer the human amyloid precursor protein Kunitz protease inhibitor domain (APPI) simultaneously for increased proteolytic stability, stronger binding affinity and improved selectivity for mesotrypsin inhibition. We identified a triple mutant APPIM17G/I18F/F34V, with a mesotrypsin inhibition constant (Ki) of 89 pM, as the strongest mesotrypsin inhibitor yet reported; this variant displays 1459-fold improved affinity, up to 350‚ÄČ000-fold greater specificity and 83-fold improved proteolytic stability compared with wild-type APPI. We demonstrated that APPIM17G/I18F/F34V acts as a functional inhibitor in cell-based models of mesotrypsin-dependent prostate cancer cellular invasiveness. Additionally, by solving the crystal structure of the APPIM17G/I18F/F34V-mesotrypsin complex, we obtained new insights into the structural and mechanistic basis for improved binding and proteolytic resistance. Our study identifies a promising mesotrypsin inhibitor as a starting point for development of anticancer protein therapeutics and establishes proof-of-principle for a novel library screening approach that will be widely applicable for simultaneously evolving proteolytic stability in tandem with desired functionality for diverse protein scaffolds.


    Organizational Affiliation

    Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trypsin-3
A, B
224Homo sapiensMutation(s): 1 
Gene Names: PRSS3 (PRSS4, TRY3, TRY4)
EC: 3.4.21.4
Find proteins for P35030 (Homo sapiens)
Go to Gene View: PRSS3
Go to UniProtKB:  P35030
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Amyloid beta A4 protein
E, C
81Homo sapiensMutation(s): 3 
Gene Names: APP (A4, AD1)
Find proteins for P05067 (Homo sapiens)
Go to Gene View: APP
Go to UniProtKB:  P05067
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.150α = 90.00
b = 78.150β = 90.00
c = 243.730γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01CA154387

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-18
    Type: Database references, Source and taxonomy
  • Version 1.2: 2016-06-01
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations