Revisiting bone morphogenetic protein-2 knuckle epitope and redesigning the epitope-derived peptides

A Structure Independent Molecular Fragment Interfuse Model for Mesoscale Dissipative Particle Dynamics Simulation of Peptides

There is a need to develop robust computational models for mesoscale simulation of the structure of peptides over large length scales toward the discovery of novel peptides for medical applications to address the issues of peptide aggregation, enzymatic degradation, and short half-life. The primary objective was to predict the structure and conformation of peptides whose native structures are not known. This work presents a new model for computation of interaction parameters between the beads in coarse-grained dissipative particle dynamics (DPD) simulation that is properly calibrated for amino acids, supports compressibility requirement of water molecules, and accounts for subtle differences in the structure of amino acids and the charge in the side chain of charged amino acids. This new model is referred to as Structure Independent Molecular Fragment Interfuse Model, abbreviated as SIMFIM, because it accounts for specific interactions between different beads, which represent molecular fragments of the amino acids, in calculating nonbonded interaction parameters in the absence of knowing the actual peptide structure. The electrostatic interactions are incorporated in this model by using a normal distribution of charges around the center of the beads to prevent the collapse of oppositely charged soft beads. The uniquely parameterized DPD force field in the SIMFIM model is optimized for a given peptide with respect to the degree of coarse-grained graining for simulating the peptide over long times and length scales. The SIMFIM model was tested in this work using four peptides, namely, TrpZip2, Rubrivinodin, Lihuanodin, and IC3-CB1/Gai peptides, whose structures were sourced from the Protein Data Bank. The SIMFIM model predicted radius of gyration (Rg) values for the peptides closer to the actual structures as compared to the conventional model, and there was less deviation between the predicted and actual structures of the peptides.

Structural Mapping of BMP Conformational Epitopes and Bioengineering Design of Osteogenic Peptides to Specifically Target the Epitope-Binding Sites

Introduction

Human bone morphogenetic proteins (BMPs) constitute a large family of cytokines related to members of the transforming growth factor-β superfamily, which fulfill biological functions by specificity binding to their cognate type I (BRI) and type II (BRII) receptors through conformational wrist and linear knuckle epitopes, respectively.

Methods and Results

We systematically examined the intermolecular recognition and interaction between the BMP proteins and BRI receptor at structural, energetic and dynamic levels. The BRI-binding site consists of three hotspot regions on BMP surface, which totally contribute ~70% potency to the BMP-BRI binding events and represent the core sections of BMP conformational wrist epitope; the contribution increases in the order: hotspot 2 (~ 8%) < hotspot 3 (~ 20%) < hotspot 1 (~ 40%). Multiple sequence alignment and structural superposition revealed a consensus sequence pattern and a similar binding mode of the three hotspots shared by most BMP members, indicating a high conservation of wrist epitope in BMP family. The three hotspots are natively folded into wellstructured U-shaped,, loop and double-stranded conformations in BMP proteins, which, however, would become largely disordered when splitting from the protein context to derive osteogenic peptides in free state, thus largely impairing their rebinding capability to BRI receptor. In this respect, cyclization strategy was employed to constrain hotspot 1/3-derived peptides into a native-like conformation, which was conducted by adding a disulfide bond across the ending arms of linear peptides based on their native conformations. Fluorescence-based assays substantiated that the cyclization can effectively improve the binding affinities of osteogenic peptides to BRI receptor by 3-6-fold. The cyclic peptides also exhibit a good selectivity for BRI over BRII (> 5-fold), confirming that they can specifically target the wrist epitope-binding site of BRI receptor.

Conclusion

The rationally designed cyclic peptides can be regarded as the promising lead entities that should be further chemically modified to enhance their in vivo biological stability for further bioengineering therapeutic osteogenic peptides against chondrocyte senescence and bone disorder.

Structural definition of the discrete hotspot sites of BMP-2 conformational wrist epitope and rational design of the hotspot-derived osteogenic peptides against chondrocyte senescence

The bone morphogenetic protein-2 (BMP-2) is an essential regulator of bone formation and remodeling, which has also been implicated in the pathogenesis of osteoarthritis and its closely related chondrocyte senescence. The BMP-2 uses a conformational wrist epitope and a linear knuckle epitope to interact with type-I (BMPR-I) and type-II (BMPR-II) receptors, respectively. Previously, the knuckle epitope has been intensely studied, but the wrist epitope still remains largely unexplored due to its discontinuous nature. In the present work, the intermolecular interaction of BMP-2 with BMPR-I was investigated systematically at structural, energetic and dynamic levels. Three discrete hotspots that represent the key BMPR-I recognition sites of BMP-2 were identified; they are spatially dispersed over the two monomers of BMP-2 dimer and totally account for 83.5 % binding potency of BMP-2 to BMPR-I (hotspot 1: residues 49-70 in monomer 1; hotspot 2: residues 24-31 in monomer 2; hotspot 3: residues 88-107 in monomer 2). Therefore, we defined the three discrete hotspot sites as the core region of wrist epitope; their contribution to the binding increases in the order: hotspot 2 < hotspot 3 < hotspot 1. We demonstrated that the primary hotspot 1 site has a native U-shaped conformation in the full-length BMP-2 protein context, but it cannot maintain in the native conformation when split from the context to obtain a free hotspot-1 peptide, thus largely impairing its binding potency to BMPR-I. We further employed disulfide-bonded cyclization and head-to-tail cyclization to constrain the peptide conformation, and found that only the former can effectively constrain the peptide into native conformation, thus considerably improving its binding affinity to BMPR-I, whereas the latter totally disorders the native conformation, thus rendering the peptide as a full nonbinder of BMPR-I.