Conformational dynamics in loop swap mutants of homologous fibronectin type III domains

Double Mutant of Chymotrypsin Inhibitor 2 Stabilized through Increased Conformational Entropy

The conformational heterogeneity of a folded protein can affect not only its function but also stability and folding. We recently discovered and characterized a stabilized double mutant (L49I/I57V) of the protein CI2 and showed that state-of-the-art prediction methods could not predict the increased stability relative to the wild-type protein. Here, we have examined whether changed native-state dynamics, and resulting entropy changes, can explain the stability changes in the double mutant protein, as well as the two single mutant forms. We have combined NMR relaxation measurements of the ps-ns dynamics of amide groups in the backbone and the methyl groups in the side chains with molecular dynamics simulations to quantify the native-state dynamics. The NMR experiments reveal that the mutations have different effects on the conformational flexibility of CI2: a reduction in conformational dynamics (and entropy estimated from this) of the native state of the L49I variant correlates with its decreased stability, while increased dynamics of the I57V and L49I/I57V variants correlates with their increased stability. These findings suggest that explicitly accounting for changes in native-state entropy might be needed to improve the predictions of the effect of mutations on protein stability.

Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics

The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or on their ability to perform wider and sometimes highly elaborated motions. Hence, there is considerable interest in the definition of accurate coarse-grained descriptions of protein dynamics, as an alternative to more computationally expensive approaches. In particular, the elastic network model, in which residue motions are subjected to pairwise harmonic potentials, is known to capture essential aspects of conformational dynamics in proteins, but has so far remained mostly phenomenological, and unable to account for the chemical specificities of amino acids. We propose, for the first time, a method to derive residue- and distance-specific effective harmonic potentials from the statistical analysis of an extensive dataset of NMR conformational ensembles. These potentials constitute dynamical counterparts to the mean-force statistical potentials commonly used for static analyses of protein structures. In the context of the elastic network model, they yield a strongly improved description of the cooperative aspects of residue motions, and give the opportunity to systematically explore the influence of sequence details on protein dynamics.

AMP-activated protein kinase β-subunit requires internal motion for optimal carbohydrate binding

AMP-activated protein kinase interacts with oligosaccharides and glycogen through the carbohydrate-binding module (CBM) containing the β-subunit, for which there are two isoforms (β(1) and β(2)). Muscle-specific β(2)-CBM, either as an isolated domain or in the intact enzyme, binds carbohydrates more tightly than the ubiquitous β(1)-CBM. Although residues that contact carbohydrate are strictly conserved, an additional threonine in a loop of β(2)-CBM is concurrent with an increase in flexibility in β(2)-CBM, which may account for the affinity differences between the two isoforms. In contrast to β(1)-CBM, unbound β(2)-CBM showed microsecond-to-millisecond motion at the base of a β-hairpin that contains residues that make critical contacts with carbohydrate. Upon binding to carbohydrate, similar microsecond-to-millisecond motion was observed in this β-hairpin and the loop that contains the threonine insertion. Deletion of the threonine from β(2)-CBM resulted in reduced carbohydrate affinity. Although motion was retained in the unbound state, a significant loss of motion was observed in the bound state of the β(2)-CBM mutant. Insertion of a threonine into the background of β(1)-CBM resulted in increased ligand affinity and flexibility in these loops when bound to carbohydrate. However, these mutations indicate that the additional threonine is not solely responsible for the differences in carbohydrate affinity and protein dynamics. Nevertheless, these results suggest that altered protein dynamics may contribute to differences in the ligand affinity of the two naturally occurring CBM isoforms.

Exposing the Moving Parts of Proteins with NMR Spectroscopy

Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool for investigating the dynamics of biomolecules since it provides a description of motion that is comprehensive, site-specific, and relatively non-invasive. In particular, the study of protein dynamics has benefited from sustained methodological advances in NMR that have expanded the scope and time scales of accessible motion. Yet, many of these advances may not be well known to the more general physical chemistry community. Accordingly, this Perspective provides a glimpse of some of the more powerful methods in liquid state NMR that are helping reshape our understanding of functional motions of proteins.

Chimeric fibronectin matrix mimetic as a functional growth- and migration-promoting adhesive substrate

Therapeutic protein engineering combines genetic, biochemical, and functional information to improve existing proteins or invent new protein technologies. Using these principles, we developed an approach to deliver extracellular matrix (ECM) fibronectin-specific signals to cells. Fibronectin matrix assembly is a cell-dependent process that converts the inactive, soluble form of fibronectin into biologically-active ECM fibrils. ECM fibronectin stimulates cell functions required for normal tissue regeneration, including cell growth, spreading, migration, and collagen reorganization. We have developed recombinant fibronectin fragments that mimic the effects of ECM fibronectin on cell function by coupling the cryptic heparin-binding fragment of fibronectin's first type III repeat (FNIII1H) to the integrin-binding domain (FNIII8-10). GST/III1H,8-10 supports cell adhesion and spreading and stimulates cell proliferation to a greater extent than plasma fibronectin. Deletion and site-specific mutant constructs were generated to identify the active regions in GST/III1H,8-10 and reduce construct size. A chimeric construct in which the integrin-binding, RGDS loop was inserted into the analogous site in FNIII8 (GST/III1H,8(RGD)), supported cell adhesion and migration, and enhanced cell proliferation and collagen gel contraction. GST/III1H,8(RGD) was expressed in bacteria and purified from soluble lysate fractions by affinity chromatography. Fibronectin matrix assembly is normally up-regulated in response to tissue injury. Decreased levels of ECM fibronectin are associated with non-healing wounds. Engineering fibronectin matrix mimetics that bypass the need for cell-dependent fibronectin matrix assembly in chronic wounds is a novel approach to stimulating cellular activities critical for tissue repair.

Structural Biology and the Design of Effective Vaccines for HIV-1 and Other Viruses

Structural biology provides a wealth of information about the three-dimensional organization and chemical makeup of proteins. An understanding of atomic-level structure offers enormous potential to design rationally proteins that stimulate specific immune responses. Yet current vaccine development efforts makes little use of structural information. At the Vaccine Research Center, a major goal is to apply structural techniques to vaccine design for challenging pathogens, that include human immunodeficiency virus type 1 (HIV-1) and other enveloped viruses such as influenza, Ebola, and respiratory syncytial viruses. Our three-part strategy involves 1.) the definition of the functional viral spike at the atomic level 2.) achieving a structural understanding of how neutralizing antibodies recognize the spike, and 3.) rational development of proteins that can elicit a specific antibody response. Overall, our strategy aims to incorporate information about viral spike-antibody interactions, to assimilate immunogenic feedback, and to leverage recent advances in immunofocusing and computational biology.

The flexibility of a distant loop modulates active site motion and product release in ribonuclease A

The role of the flexible loop 1 in protein conformational motion and in the dissociation of enzymatic product from ribonuclease A (RNase A) was investigated by creation of a chimeric enzyme in which a 6-residue loop 1 from the RNase A homologue, eosinophil cationic protein (ECP), replaced the 12-residue loop 1 in RNase A. The chimera (RNase A(ECP)) experiences only local perturbations in NMR backbone chemical shifts compared to WT RNase A. Many of the flexible residues that were previously identified in WT as involved in an important conformational change now experience no NMR-detected millisecond motions in the chimera. Likewise, binding of the product analogue, 3'-CMP, to RNase A(ECP) results in only minor chemical shift changes in the enzyme similar to what is observed for the H48A mutant of RNase A and in contrast to WT enzyme. For both RNase A(ECP) and H48A there is a 10-fold decrease in the product release rate constant, k(off), compared to WT, in agreement with previous studies indicating the importance of flexibility in RNase A in the overall rate-limiting product release step. Together, these NMR and biochemical experiments provide additional insight into the mechanism of millisecond motions in the RNase A catalytic cycle.

FN3: a new protein scaffold reaches the clinic

In the ten years since the first fibronectin type III (FN3) domain library was published, FN3 has continued to show promise as a scaffold for the generation of stable protein domains that bind to targets with high affinity. A variety of display systems, library designs and affinity maturation strategies have been used to generate FN3 domains with nanomolar to picomolar affinities. The first crystal structures of engineered FN3 molecules in complex with their targets have been solved, and structural studies of engineered FN3 have begun to reveal determinants of stability and to define zones that accept mutations with minimal trade-off between affinity and stability. CT-322, the first engineered FN3 to enter clinical development, is now entering Phase II trials for glioblastoma multiforme.

Transient opening of fibronectin type III (FNIII) domains: the interaction of the third FNIII domain of FN with anastellin

We previously reported that the fibronectin (FN) type III domains of FN may unfold to interact with anastellin and form FN aggregates. In the present study, we have focused on the interaction between anastellin and the third FN type III domain (III3), which is a key anastellin binding site on FN. Anastellin binding to III3 was monitored by 8-anilino-1-naphthalene sulfonate (ANS) fluorescence. ANS binding to anastellin dramatically increased its emission intensity, but this was reduced to half by the addition of III3, suggesting that ANS and III3 share a common hydrophobic binding site on anastellin. An engineered mutant of III3 that was stabilized by an intrachain disulfide bond did not interact with anastellin, as seen by its failure to interfere with ANS binding to anastellin. We also mutated hydrophobic core residues to destabilize III3 and found that these mutants were still capable of interacting with anastellin. Anastellin binding to III3 was also monitored using an intramolecular green fluorescent protein (GFP)-based fluorescence resonance energy transfer (FRET) construct, in which III3 was flanked by two GFP variants (III3-FRET). Anastellin bound to III3-FRET and caused an increase in the FRET signal. The dissociation constant was estimated to be approximately 210 nM. The binding kinetics of anastellin to III3-FRET fit a first-order reaction with a half-time of approximately 30 s; the kinetics with destabilized III3 mutants were even faster. Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry suggested that the middle part of III3 became destabilized and protease sensitive upon anastellin binding. Thus, the stability of III3 seems to be a key factor in anastellin binding.

Role of loop-loop interactions in coordinating motions and enzymatic function in triosephosphate isomerase

The enzyme triosephosphate isomerase (TIM) has been used as a model system for understanding the relationship between protein sequence, structure, and biological function. The sequence of the active site loop (loop 6) in TIM is directly correlated with a conserved motif in loop 7. Replacement of loop 7 of chicken TIM with the corresponding loop 7 sequence from an archaeal homologue caused a 10(2)-fold loss in enzymatic activity, a decrease in substrate binding affinity, and a decrease in thermal stability. Isotope exchange studies performed by one-dimensional (1)H NMR showed that the substrate-derived proton in the enzyme is more susceptible to solvent exchange for DHAP formation in the loop 7 mutant than for WT TIM. TROSY-Hahn Echo and TROSY-selected R(1rho) experiments indicate that upon mutation of loop 7, the chemical exchange rate for active site loop motion is nearly doubled and that the coordinated motion of loop 6 is reduced relative to that of the WT. Temperature dependent NMR experiments show differing activation energies for the N- and C-terminal hinges in this mutant enzyme. Together, these data suggest that interactions between loop 6 and loop 7 are necessary to provide the proper chemical context for the enzymatic reaction to occur and that the interactions play a significant role in modulating the chemical dynamics near the active site.

Protein conformational flexibility prediction using machine learning

Using a data set of 16 proteins, a neural network has been trained to predict backbone 15N generalized order parameters from the three-dimensional structures of proteins. The final network parameterization contains six input features. The average prediction accuracy, as measured by the Pearson's correlation coefficient between experimental and predicted values of the square of the generalized order parameter is >0.70. Predicted order parameters for non-terminal amino acid residues depends most strongly on the local packing density and the probability that the residue is located in regular secondary structure.

Structure and dynamics of Ca2+-binding domain 1 of the Na+/Ca2+ exchanger in the presence and in the absence of Ca2+

The Na(+)/Ca(2+) exchanger is the major exporter of Ca(2+) across the cell membrane of cardiomyocytes. The activity of the exchanger is regulated by a large intracellular loop that contains two Ca(2+)-binding domains, calcium-binding domain (CBD) 1 and CBD2. CBD1 binds Ca(2+) with much higher affinity than CBD2 and is considered to be the primary Ca(2+) sensor. The effect of Ca(2+) on the structure and dynamics of CBD1 has been characterized by NMR spectroscopy using chemical shifts, residual dipolar couplings, and spin relaxation. Residual dipolar couplings are used in a new way for residue selection in the determination of the anisotropic rotational diffusion tensor from spin relaxation data. The results provide a highly consistent description across these complementary data sets and show that Ca(2+) binding is accompanied by a selective conformational change among the binding site residues. Residues that exhibit a significant conformational change are also sites of altered dynamics. In particular, Ca(2+) binding restricts the mobility of the major acidic segment and affects the dynamics of several nearby binding loops. These observations indicate that Ca(2+) elicits a local transition to a well-ordered coordination geometry in the CBD1-binding site.

Crosstalk between the protein surface and hydrophobic core in a core-swapped fibronectin type III domain

Two homologous fibronectin type III (fnIII) domains, FNfn10 (the 10th fnIII domain of human fibronectin) and TNfn3 (the third fnIII domain of human tenascin), have essentially the same backbone structure, although they share only ∼ 24% sequence identity. While they share a similar folding mechanism with a common core of key residues in the folding transition state, they differ in many other physical properties. We use a chimeric protein, FNoTNc, to investigate the molecular basis for these differences. FNoTNc is a core-swapped protein, containing the “outside” (surface and loops) of FNfn10 and the hydrophobic core of TNfn3. Remarkably, FNoTNc retains the structure of the parent proteins despite the extent of redesign, allowing us to gain insight into which components of each parent protein are responsible for different aspects of its behaviour. Naively, one would expect properties that appear to depend principally on the core to be similar to TNfn3, for example, the response to mutations, folding kinetics and side-chain dynamics, while properties apparently determined by differences in the surface and loops, such as backbone dynamics, would be more like FNfn10. While this is broadly true, it is clear that there are also unexpected crosstalk effects between the core and the surface. For example, the anomalous response of FNfn10 to mutation is not solely a property of the core as we had previously suggested.