ucleation step, followed by a rapid elongation phase. The nucleation step regulates assembly. If too many nuclei form, the growing complexes will deplete the dimer pool and the reaction will end up with trapped, incomplete intermediates. Mass spectrometry has detected the predicted large intermediates when assembly takes place under extreme conditions. Critical to interpreting any assembly data is the understanding that assembly is allosterically regulated. Cp undergoes conformational c-Met inhibitor 2 biological activity change to become assembly active to participate in assembly. In vitro assembly is promoted by increasing ionic strength. Ionic strength changes in the range 
of 100 to 1000 mM may act by suppressing long-range electrostatic repulsion or may induce Cp conformation to an assembly-active state. In support of the latter possibility, zinc ions induce conformational change and trigger assembly at micromolar concentrations. Mis-regulation of assembly has also been observed with small molecules, which is the basis for the development of the allosteric modulators that will be discussed later in this review. Mutants provide insight into the basis of allosteric change in Cp. For example, an assembly-incompetent Cp mutant was designed to take advantage of Y132, a residue on the exterior of a dimer that becomes buried during assembly and contributes about 10% of the hydrophobic surface at a dimer-dimer interface. When it is replaced by alanine, the resulting protein was unable to nucleate capsid assembly but could co-assemble with wild type Cp to form morphologically normal capsids that were fragile, suggesting that the mutation weakened interfacial association energies. Similarly, the V124W mutant increases buried hydrophobic surface and the strength of association energy proportionately while V124A decreases both. However, in addition to the expected change in association energy, there is an unexpected change in the hydrodynamic Author Manuscript Author Manuscript Author Manuscript Author Manuscript Antiviral Res. Author manuscript; available in PMC 2016 September 01. Zlotnick et al. Page 7 radius of dimer, observed by size exclusion chromatography, which indicates that Y132A and V124A are less compact than wt and V124W is more compact. That is, these side chains, presumably on the exterior of the Cp dimer PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19854301 affect the protein’s structure an indication of allosteric change. Similar behavior is seen in mutations distant from the inter-dimer interface, i.e. at the intradimer interface. These mutations affect assembly kinetics and thermodynamics, indicating that changes in Cp dimer conformation can up- or down-regulate assembly. An intradimer disulfide bond, between dimer-related cysteine 61 residues at the center of the four helix bundle, is reported to cause slow assembly kinetics and decreased capsid stability. Conversely, a naturally occurring mutation F/I 97L, located near C61, enhances assembly rate and extent in vitro while in vivo leads to secretion of immature ssDNA-containing virions. Assembly of F97L shows a substantially more positive enthalpy of assembly though the interdimer contact is unchanged, suggesting the mutation changes Cp dimer conformation or dynamical range of conformations. Two other mutations distant from the inter-dimer interface, F23A and L42A, stabilize dimers and inhibit capsid formation, presumably by affecting the dynamic conformation of Cp. The effects of errors in assembly are pleiotropic. Timing is critical for in vivo core assembly, whi
