Rational design of a calcium-binding protein

Calcium ions play key roles as structural components in biomineralization and as a second messenger in signaling pathways. We have introduced a de novo designed calcium-binding site into the framework of a non-calcium-binding protein, domain 1 of CD2. The resulting protein selectively binds calcium over magnesium with calcium-binding affinity comparable to that of natural extracellular calcium-binding proteins (K(d) of 50 microM). This experiment is the first successful metalloprotein design that has a high coordination number (seven) metal-binding site constructed into a beta-sheet protein. Our results demonstrate the feasibility of designing a single calcium-binding site into a host protein, taking into account only local properties of a calcium-binding site obtained by a survey of natural calcium-binding proteins and chelators. The resulting site exhibits strong metal selectivity, suggesting that it should now be feasible to understand and manipulate signaling processes by designing novel calcium-modulated proteins with specifically desired functions and to affect their stability.     

Probing site-specific calmodulin calcium and lanthanide affinity by grafting

Ca2+ binding is essential for the biological functions of calmodulin (CaM) as a trigger/sensor protein to regulate many biological processes in the Ca2+ -signaling cascade. A challenge in understanding the mechanism of Ca2+ signaling is to obtain site-specific information about the Ca2+ binding properties of individual Ca2+ -binding sites of EF-hand proteins, especially for CaM. In this paper, we report the first estimation of the intrinsic Ca2+ affinities of the four EF-hand loops of calmoduin (I-IV) by individually grafting into the domain 1 of CD2. Taking advantage of the Trp residues in the host protein, we first determined metal-binding affinities for Tb3+, Ca2+, and La3+ for all four grafted EF-loops using Tb3+ aromatic resonance energy transfer. EF-loop I exhibits the strongest binding affinity for Ca2+, La3+, and Tb3+, while EF-loop IV has the weakest metal-binding affinity. EF-loops I-IV of CaM have dissociation constants for Ca2+ of 34, 245, 185, and 814 microM, respectively, with the order I > III approximately equal to II > IV. These findings support a charge-ligand-balanced model in which both the number of negatively charged ligand residues and the balanced electrostatic dentate-dentate repulsion by the adjacent charged residues are two major determinants for the relative Ca2+ -binding affinities of EF-loops in CaM. Our grafting method provides a new strategy to obtain site-specific Ca2+ binding properties and a better estimation of the cooperativity and conformational change contributions of coupled EF-hand proteins.     

Metal ion binding to parvalbumin. A proton NMR study

The 1H NMR spectra of carp parvalbumin saturated with Ca2+, Cd2+, La3+ and Lu3+ were compared, using 2D 1H NMR techniques as well as conventional 1H NMR spectra. The Ca2+ and Cd2+ saturated parvalbumin (with both high affinity Ca2+-binding sites occupied) gave rise to very similar spectra. This shows that these two species have almost identical protein conformations. The 1H NMR spectrum from the Ln3+ saturated parvalbumins deviated from the other two and it was therefore concluded that Cd2+ is a better probe for Ca2+ than Ln3+ in parvalbumin and probably also for related calcium binding proteins. The addition of excess of divalent metal ions, such as Mg2+ or Ca2+, causes small changes in the chemical shift of some methyl resonances. This is presumably caused by binding of these metal ions to a third site close to the CD site which is made up of the carboxylic groups from Glu 60 and Asp 61.     

Secondary ligands enhance affinity at a designed metal-binding site.

BACKGROUND: Specific interactions of metal ions with proteins are central to all life processes. The varied functions enabled by this cooperation are a consequence of strict control of the binding-site environment, particularly the number, type and geometry of metal-coordinating sidechains. Attempts to mimic these characteristics in the de novo design of metal-binding sites have thus far concentrated primarily on metal recruitment and not on affecting site function through systematic fine-tuning of the metal environment. RESULTS: A designed tetrahedral Zn(II)-binding site in a variant of the B1 domain of IgG-binding protein G has been expanded by introducing 'secondary ligands'. These interactions were engineered to stabilize the positions of the metal-coordinating histidine residues while retaining the desired coordination geometry. Each mutation increased the protein's affinity for metal, and combining two secondary ligands demonstrated that these enhancements are additive. These results mimic the effects of altering similar interactions observed in the native Zn(II)-binding site of carbonic anhydrase. In the B1 system, this enhanced affinity for metal is observed despite a substantial decrease in protein secondary structure. CONCLUSIONS: The intended effects of secondary ligand addition on metal affinity were observed in each mutant and demonstrated to be additive. Addition of metal also stabilized the protein's structure, partially offsetting the destabilizing effect of the mutations. These results represent a successful first attempt at designing an extended metal-binding site environment and illustrate the importance of including secondary interactions in the design of metal-binding sites.     

Factors governing the substitution of La3+ for Ca2+ and Mg2+ in metalloproteins: a DFT/CDM study

Trivalent lanthanide cations are extensively being used in biochemical experiments to probe various dication-binding sites in proteins; however, the factors governing the binding specificity of lanthanide cations for these binding sites remain unclear. Hence, we have performed systematic studies to evaluate the interactions between La3+ and model Ca2+ - and Mg2+ -binding sites using density functional theory combined with continuum dielectric methods. The calculations reveal the key factors and corresponding physical bases favoring the substitution of trivalent lanthanides for divalent Ca2+ and Mg2+ in holoproteins. Replacing Ca2+ or Mg2+ with La3+ is facilitated by (1) minimizing the solvent exposure and the flexibility of the metal-binding cavity, (2) freeing both carboxylate oxygen atoms of Asp/Glu side chains in the metal-binding site so that they could bind bidentately to La3+, (3) maximizing the number of metal-bound carboxylate groups in buried sites, but minimizing the number of metal-bound carboxylate groups in solvent-exposed sites, and (4) including an Asn/Gln side chain for sites lined with four Asp/Glu side chains. In proteins bound to both Mg2+ and Ca2+, La3+ would prefer to replace Ca2+, as compared to Mg2+. A second Mg2+-binding site with a net positive charge would hamper the Mg2+ --> La3+ exchange, as compared to the respective mononuclear site, although the La3+ substitution of the first native metal is more favorable than the second one. The findings of this work are in accord with available experimental data.     

Organic Ligand Binding by a Hydrophobic Cavity in a Designed Tetrameric Coiled‐Coil Protein

The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled‐coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand‐binding characteristics of the cavities, we originally designed two other coiled‐coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size‐complementary organic compounds. The dissociation constants, K_d, of AM2W were 220 nM for adamantane, 81 μM for 1‐adamantanol, and 294 μM for 1‐adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.     

A De Novo-Designed Type 3 Copper Protein Tunes Catechol Substrate Recognition and Reactivity

De novo metalloprotein design is a remarkable approach to shape protein scaffolds toward specific functions. Here, we report the design and characterization of Due Rame 1 (DR1), a de novo designed protein housing a di-copper site and mimicking the Type 3 (T3) copper-containing polyphenol oxidases (PPOs). To achieve this goal, we hierarchically designed the first and the second di-metal coordination spheres to engineer the di-copper site into a simple four-helix bundle scaffold. Spectroscopic, thermodynamic, and functional characterization revealed that DR1 recapitulates the T3 copper site, supporting different copper redox states, and being active in the O₂-dependent oxidation of catechols to o-quinones. Careful design of the residues lining the substrate access site endows DR1 with substrate recognition, as revealed by Hammet analysis and computational studies on substituted catechols. This study represents a premier example in the construction of a functional T3 copper site into a designed four-helix bundle protein.     

Characterization of a discontinuous epitope of the HIV envelope protein gp120 recognized by a human monoclonal antibody using chemical modification and mass spectrometric analysis

A subset of the neutralizing anti-HIV antibodies recognize epitopes on the envelope protein gp120 of the human immunodeficiency virus. These epitopes are exposed during conformational changes when gp120 binds to its primary receptor CD4. Based on chemical modification of lysine and arginine residues followed by mass spectrometric analysis, we determined the epitope on gp120 recognized by the human monoclonal antibody 559/64-D, which was previously found to be specific for the CD4 binding domain. Twenty-four lysine and arginine residues in recombinant full-length glycosylated gp120 were characterized; the relative reactivities of two lysine residues and five arginine residues were affected by the binding of 559/64-D. The data show that the epitope is discontinuous and is located in the proximity of the CD4-binding site. Additionally, the reactivities of a residue that is located in the secondary receptor binding region and several residues distant from the CD4 binding site were also altered by Ab binding. These data suggest that binding of 559/64-D induced conformational changes which result in altered surface exposure of specific amino acids distant from the CD4-binding site. Consequently, binding of 559/64-D to gp120 affects not only the CD4-binding site, which is recognized as the epitope, but appears to have a global effect on surface exposed residues of the full-length glycosylated gp120.     

全新设计蛋白质的折叠机制

蛋白质全新设计和折叠研究是从两个不同的方向来理解蛋白质序列-结构-功能关系这一结构生物学重要问题. 蛋白质全新设计取得的成功实例一定程度上检验了人们对蛋白质结构和相互作用理解的准确性, 但它们中多数所表现的不同于天然蛋白质的折叠动力学特征也表明, 要达到最终的功能化实现目标还面临着不少的挑战. 本文综述了蛋白质全新设计的发展过程及现状, 蛋白质折叠研究在实验、理论及模拟方面的研究进展, 以及全新设计蛋白质的折叠机制的研究现状. 阐述了深入了解全新设计蛋白质与天然蛋白质折叠机制的不同, 可以为进一步有效地合理化设计蛋白质提供有益的参考.     

Designing sequence to control protein function in an EF-hand protein

The extent of conformational change that calcium binding induces in EF-hand proteins is a key biochemical property specifying Ca(2+) sensor versus signal modulator function. To understand how differences in amino acid sequence lead to differences in the response to Ca(2+) binding, comparative analyses of sequence and structures, combined with model building, were used to develop hypotheses about which amino acid residues control Ca(2+)-induced conformational changes. These results were used to generate a first design of calbindomodulin (CBM-1), a calbindin D(9k) re-engineered with 15 mutations to respond to Ca(2+) binding with a conformational change similar to that of calmodulin. The gene for CBM-1 was synthesized, and the protein was expressed and purified. Remarkably, this protein did not exhibit any non-native-like molten globule properties despite the large number of mutations and the nonconservative nature of some of them. Ca(2+)-induced changes in CD intensity and in the binding of the hydrophobic probe, ANS, implied that CBM-1 does undergo Ca(2+) sensorlike conformational changes. The X-ray crystal structure of Ca(2+)-CBM-1 determined at 1.44 A resolution reveals the anticipated increase in hydrophobic surface area relative to the wild-type protein. A nascent calmodulin-like hydrophobic docking surface was also found, though it is occluded by the inter-EF-hand loop. The results from this first calbindomodulin design are discussed in terms of progress toward understanding the relationships between amino acid sequence, protein structure, and protein function for EF-hand CaBPs, as well as the additional mutations for the next CBM design.     

Mobility Study of Individual Residue Sites in the Carbohydrate Recognition Domain of LSECtin Using SDSL–EPR Technique

Conformational changes in proteins profoundly influence their functional profiles. With site-directed spin labeling (SDSL)?Celectron paramagnetic resonance (EPR) spectroscopy, we investigated the mobility features of individual residue sites in the carbohydrate recognition domain (CRD) of LSECtin, a type II integral membrane protein. The mobility of six different residue sites scatting around the Ca²⁺-1-binding site were investigated by comparing their EPR spectra rotational correlation time ?? _c in order to obtain the information of conformational changes of relevant region. The results showed that the overall mobility of LSECtin-CRD increased after addition of Ca²⁺ and N-acetylglucosamine, but different sites in the CRD exhibited different mobility features, suggesting that these sites may have different functional profiles. The preliminary observations thus demonstrated that SDSL?CEPR spectroscopy is not only an effective technique to reveal the mobility of single residue sites in LSECtin-CRD but also that the functions of single residue sites may be indicated by their conformational dynamics.     

A photoactivable probe for calcium binding proteins

Ca2+ as a signaling molecule carries information pivotal to cell life and death via its reversible interaction with a specific site in a protein. Although numerous Ca2+-dependent activities are known, the proteins responsible for some of these activities remain unidentified. We synthesized and characterized a photoreactive reagent, azido ruthenium (AzRu), which interacts specifically with Ca2+ binding proteins and strongly inhibits their Ca2+-dependent activities, regardless of their catalytic mechanisms or functional state as purified proteins, embedded in the membrane or in intact cells. As expected from a Ca2+ binding protein-specific reagent, AzRu had no effect on Ca2+-independent and Mg2+-dependent activities. Az103Ru covalently bound, and specifically labeled, known Ca2+ binding proteins. AzRu is a photoreactive reagent that provides an approach for identification of Ca2+ binding proteins, characterization of their binding sites, and exploration of new Ca2+-dependent processes.     

Metalloprotein and metallo-DNA/RNAzyme design: current approaches, success measures, and future challenges

Specific metal-binding sites have been found in not only proteins but also DNA and RNA molecules. Together these metalloenzymes consist of a major portion of the enzyme family and can catalyze some of the most difficult biological reactions. Designing these metalloenzymes can be both challenging and rewarding because it can provide deeper insights into the structure and function of proteins and cheaper and more stable alternatives for biochemical and biotechnological applications. Toward this goal, both rational and combinatorial approaches have been used. The rational approach is good for designing metalloenzymes that are well characterized, such as heme proteins, while the combinatorial approach is better at designing those whose structures are poorly understood, such as metallo-DNA/RNAzymes. Among the rational approaches, de novo design is at its best when metal-binding sites reside in a scaffold whose structure has been designed de novo (e.g., alpha-helical bundles). Otherwise, design using native scaffolds can be equally effective, allowing more choices of scaffolds whose structural stability is often more resistant to multiple mutations. In addition, computational and empirical designs have both enjoyed successes. Because of the limitation in defining structural parameters for metal-binding sites, a computational approach is restricted to mostly metal-binding sites that are well defined, such as mono- or homonuclear centers. An empirical approach, even though it is less restrictive in the metal-binding sites to be designed, depends heavily on one's knowledge and choice of templates and targets. An emerging approach is a combination of both computational and empirical approaches. The success of these approaches can be measured not only by three-dimensional structural comparison between the designed and target enzymes but also by the total amount of insight obtained from the design process and studies of the designed enzymes. One of the biggest advantages of designed metalloenzymes is the potential of placing two different metal-binding sites in the same protein framework for comparison. A final measure of success is how one can utilize the insight gained from the intellectual exercise to design new metalloenzymes, including those with unprecedented structures and functions. Future challenges include designing more complex metalloenzymes such as heteronuclear metal centers with strong nanomolar or better affinities. A key to meeting this challenge is to focus on the design of not only primary but also secondary coordination spheres using a combination of improved computer programs, experimental design, and high-resolution crystallography.     

Effects of Ca2+, Zn2+ and Cd2+ on uridine diphosphate-glucuronyltransferase and beta-glucuronidase activities in rat liver microsomes

The effect of various metals on uridine diphosphate (UDP)-glucuronyltransferase and beta-glucuronidase activities in rat liver microsomes was investigated. The presence of Mn2+, Cd2+, Zn2+, V5+, Ni2+, Co2+, Cu+ or Ca2+ (20 microM) in the enzyme reaction mixture did not cause a significant alteration of UDP-glucuronyltransferase activity in hepatic microsomes. Of these metals, Zn2+ and Cd2+ (20 microM) caused a remarkable increase in hepatic microsomal beta-glucuronidase activity. Appreciable effects of Zn2+ and Cd2+ on beta-glucuronidase activity were seen at 5.0 microM, and the effects were saturated at 50 microM. Ca2+ (5.0-50 microM) and/or the Ca2(+)-binding protein regucalcin (2.0 microM) did not have an appreciable effect on UDP-glucuronyltransferase and beta-glucuronidase activities in hepatic microsomes. Thus, Zn2+ and Cd2+ uniquely increased beta-glucuronidase activity. The Zn2(+)- and Cd2(+)-induced increase in beta-glucuronidase activity was completely reversed by the presence of an SH group-protecting reagent (dithiothreitol). The response of the microsomal enzyme to Zn2+ and Cd2+ (20 microM) was no longer seen after treatment with 0.2% Triton X-100 [polyoxyethylene(10)octylphenyl ether], indicating that the stimulation by these metals is dependent on membrane association. The present study suggests that, of various metals tested, Zn2+ and Cd2+ can uniquely increase hepatic microsomal beta-glucuronidase activity and that their effect is based on binding to membranous SH groups, beside the enzyme protein.     

Spectroscopic and computational studies of the de novo designed protein DF2t: correlation to the biferrous active site of ribonucleotide reductase and factors that affect O2 reactivity

DF2t, a de novo designed protein that mimics the active-site structure of many non-heme biferrous enzymes, has been studied using a combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature variable-field (VTVH) MCD. The active site of DF2t is found to have one five-coordinate iron and one four-coordinate iron, which are weakly antiferromagnetically coupled through a mu-1,3 carboxylate bridge. These results bear a strong resemblance to the spectra of Escherichia coli ribonucleotide reductase (R2), and density functional theory calculations were conducted on the W48F/D84E R2 mutant in order to determine the energetics of formation of a monodentate end-on-bound O2 to one iron in the binuclear site. The mu-1,3 carboxylate bridges found in O2-activating enzymes lack efficient superexchange pathways for the second electron transfer (i.e., the OH/oxo bridge in hemerythrin), and simulations of the binding of O2 in a monodentate end-on manner revealed that the bridging carboxylate ligands do not appear capable of transferring an electron to O2 from the remote Fe. Comparison of the results from previous studies of the mu-1,2 biferric-peroxo structure, which bridges both irons, finds that the end-on superoxide mixed-valent species is considerably higher in energy than the bridging peroxo-diferric species. Thus, one of the differences between O2-activating and O2-binding proteins appears to be the ability of O2 to bridge both Fe centers to generate a peroxo intermediate capable of further reactivity.     

De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex

The de novo design of membrane proteins remains difficult despite recent advances in understanding the factors that drive membrane protein folding and association. We have designed a membrane protein PRIME (PoRphyrins In MEmbrane) that positions two non-natural iron diphenylporphyrins (Fe(III)DPP's) sufficiently close to provide a multicentered pathway for transmembrane electron transfer. Computational methods previously used for the design of multiporphyrin water-soluble helical proteins were extended to this membrane target. Four helices were arranged in a D(2)-symmetrical bundle to bind two Fe(II/III) diphenylporphyrins in a bis-His geometry further stabilized by second-shell hydrogen bonds. UV-vis absorbance, CD spectroscopy, analytical ultracentrifugation, redox potentiometry, and EPR demonstrate that PRIME binds the cofactor with high affinity and specificity in the expected geometry.     

An approximate method in using molecular mechanics simulations to study slow protein conformational changes

The broad range of characteristic motions in proteins has limited the applicability of molecular dynamics simulations in studying large-scale conformational transitions. We present an approximate method, making use of standard MD simulations and using a much larger integration time step, to obtain the structural changes for slow systematic motions of large complex systems. We show the applicability of this method by simulating the open to closed Calmodulin calcium binding domain conformational changes. Starting with the Ca2+-bound X-ray structure, and after the removal of the Ca2+ ions, our calculation yielded intermediate conformations during the rearrangement of helices in each Ca2+ binding pocket, leading to a structure with a lowest rmsd of 1.56 A compared to the NMR apo-calmodulin structure.     

pH值和钙离子对尖吻蝮蛇抗血小板凝集素二级结构的影响

尖吻蝮蛇毒中抗血小板凝集素是凝血因子IX/凝血因子X结合蛋白，它具有抗凝血和抑制血小板凝集双重活性。用红外光谱、拉曼光谱和CD谱研究了抗血小板凝集素的二级结构以及pH值和钙离子对其二级结构的影响。用CD谱测得，在水溶液中，抗血小板凝集素的主要骨架构象为β-折叠(26.3%)和α-螺旋(19.6%)结构。拉曼光谱显示，在粉末状态，其α-螺旋含量显著降低。CD谱还表明，抗血小板凝集素在pH值3.0～11.0范围内保持稳定的天然结构，钙离子诱导的抗血小板凝集素结构变化是可逆的，钙离子在稳定抗血小板凝集素的天然结构中起重要作用。     

Ca2+ -dependent regulation of phototransduction

Photon absorption by rhodopsin triggers the phototransduction signaling pathway that culminates in degradation of cGMP, closure of cGMP-gated ion channels and hyperpolarization of the photoreceptor membrane. This process is accompanied by a decrease in free Ca(2+) concentration in the photoreceptor cytosol sensed by Ca(2+)-binding proteins that modulate phototransduction and activate the recovery phase to reestablish the photoreceptor dark potential. Guanylate cyclase-activating proteins (GCAPs) belong to the neuronal calcium sensor (NCS) family and are responsible for activating retinal guanylate cyclases (retGCs) at low Ca(2+) concentrations triggering synthesis of cGMP and recovery of the dark potential. Here we review recent structural insight into the role of the N-terminal myristoylation in GCAPs and compare it to other NCS family members. We discuss previous studies identifying regions of GCAPs important for retGC1 regulation in the context of the new structural data available for myristoylated GCAP1. In addition, we present a hypothetical model for the Ca(2+)-triggered conformational change in GCAPs and retGC1 regulation. Finally, we briefly discuss the involvement of mutant GCAP1 proteins in the etiology of retinal degeneration as well as the importance of other Ca(2+) sensors in the modulation of phototransduction.