An-Suei Yang

Free Energy Balance in Protein Folding

Publisher Summary This chapter suggests a particular decomposition that relies on classical concepts and that is intuitively straightforward. It aims to provide a semi-quantitative basis for the interpretation of experiments. These include thermodynamic studies of the entire folding process, experiments based on site-directed mutagenesis that attempt to isolate the free energy contributions of individual groups and studies of folding intermediates. A fundamental problem in any attempt at analysis is that the free energy change associated with protein folding is usually described in terms of forces that are much larger than their resultant. The chapter aims to arrive at a model capable of accounting for the small free energy changes that accompany protein folding while providing a more quantitative description of the effects of single-site mutations. The approach is to characterize individual forces by extracting information as to their magnitudes from direct measurements on proteins, from the principles of physical chemistry, and from the methods of continuum electrostatics. The relevant theory and experimental data are discussed individually and an attempt has been made to extract some general principles about protein folding.

CHARACTERIZATION OF THE INTERACTION BETWEEN THE WILSON AND MENKES DISEASE PROTEINS AND THE CYTOPLASMIC COPPER CHAPERONE, HAH1P

Wilson disease (WD) and Menkes disease (MNK) are inherited disorders of copper metabolism. The genes that mutate to give rise to these disorders encode highly homologous copper transporting ATPases. We use yeast and mammalian two-hybrid systems, along with anin vitro assay to demonstrate a specific, copper-dependent interaction between the six metal-binding domains of the WD and MNK ATPases and the cytoplasmic copper chaperone HAH1. We demonstrate that several metal-binding domains interact independently or in combination with HAH1p, although notably domains five and six of WDp do not. Alteration of either the Met or Thr residue of the HAH1p MTCXXC motif has no observable effect on the copper-dependent interaction, whereas alteration of either of the two Cys residues abolishes the interaction. Mutation of any one of the HAH1p C-terminal Lys residues (Lys56, Lys57, or Lys60) to Gly does not affect the interaction, although deletion of the 15 C-terminal residues abolishes the interaction. We show that apo-HAH1p can bind in vitroto copper-loaded WDp, suggesting reversibility of copper transfer from HAH1p to WD/MNKp. The in vitro HAH1/WDp interaction is metalospecific; HAH1 preincubated with Cu2+ or Hg+ but not with Zn2+, Cd2+, Co2+, Ni3+, Fe3+, or Cr3+ interacted with WDp. Finally, we model the protein-protein interaction and present a theoretical representation of the HAH1p·Cu·WD/MNKp complex.

Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors.

The site on the HIV-1 gp120 glycoprotein that binds the CD4 receptor is recognized by broadly reactive antibodies, several of which neutralize over 90% of HIV-1 strains. To understand how antibodies achieve such neutralization, we isolated CD4-binding-site (CD4bs) antibodies and analyzed 16 co-crystal structures -8 determined here- of CD4bs antibodies from 14 donors. The 16 antibodies segregated by recognition mode and developmental ontogeny into two types: CDR H3-dominated and VH-gene-restricted. Both could achieve greater than 80% neutralization breadth, and both could develop in the same donor. Although paratope chemistries differed, all 16 gp120-CD4bs antibody complexes showed geometric similarity, with antibody-neutralization breadth correlating with antibody-angle of approach relative to the most effective antibody of each type. The repertoire for effective recognition of the CD4 supersite thus comprises antibodies with distinct paratopes arrayed about two optimal geometric orientations, one achieved by CDR H3 ontogenies and the other achieved by VH-gene-restricted ontogenies.

The Na+ Channel Inactivation Gate Is a Molecular Complex: A Novel Role of the COOH-terminal Domain

Electrical activity in nerve, skeletal muscle, and heart requires finely tuned activity of voltage-gated Na+ channels that open and then enter a nonconducting inactivated state upon depolarization. Inactivation occurs when the gate, the cytoplasmic loop linking domains III and IV of the α subunit, occludes the open pore. Subtle destabilization of inactivation by mutation is causally associated with diverse human disease. Here we show for the first time that the inactivation gate is a molecular complex consisting of the III-IV loop and the COOH terminus (C-T), which is necessary to stabilize the closed gate and minimize channel reopening. When this interaction is disrupted by mutation, inactivation is destabilized allowing a small, but important, fraction of channels to reopen, conduct inward current, and delay cellular repolarization. Thus, our results demonstrate for the first time that physiologically crucial stabilization of inactivation of the Na+ channel requires complex interactions of intracellular structures and indicate a novel structural role of the C-T domain in this process.

Analysis of the heat capacity dependence of protein folding

This paper presents an analysis of plots of enthalpy versus heat capacity change at 25 degrees C for the unfolding of proteins and for the dissolution of gaseous, liquid and solid solutes, first reported by Murphy, Privalov & Gill. The negative slope in the enthalpy plot for proteins is interpreted as arising from a large penalty associated with burying polar groups in the protein interior. The small enthalpy changes that accompany protein unfolding at 25 degrees C are also discussed. It is argued that the combined effects of hydrogen bond formation and close packing predict a large positive enthalpy of unfolding. Electrostatic calculations indicate that the penalty associated with burying polar groups is large enough to effectively cancel these terms, leading to the small net enthalpy changes that are observed. The free energy changes associated with protein folding are also discussed. The free energy cost of burying polar groups largely compensates for the stabilizing contribution of the hydrophobic effect and would appear to account for the fact that proteins are marginally stable, independent of their size and of their relative hydrophobicities.

Electrostatic Contributions to the Binding Free Energy of the λcI Repressor to DNA

Abstract A model based on the nonlinear Poisson-Boltzmann (NLPB) equation is used to study the electrostatic contribution to the binding free energy of the λ cI repressor to its operator DNA. In particular, we use the Poisson-Boltzmann model to calculate the pK a shift of individual ionizable amino acids upon binding. We find that three residues on each monomer, Glu 34 , Glu 83 , and the amino terminus, have significant changes in their pK a and titrate between pH 4 and 9. This information is then used to calculate the pH dependence of the binding free energy. We find that the calculated pH dependence of binding accurately reproduces the available experimental data over a range of physiological pH values. The NLPB equation is then used to develop an overall picture of the electrostatics of the λ cI repressor–operator interaction. We find that long-range Coulombic forces associated with the highly charged nucleic acid provide a strong driving force for the interaction of the protein with the DNA. These favorable electrostatic interactions are opposed, however, by unfavorable changes in the solvation of both the protein and the DNA upon binding. Specifically, the formation of a protein-DNA complex removes both charged and polar groups at the binding interface from solvent while it displaces salt from around the nucleic acid. As a result, the electrostatic contribution to the λ cI repressor–operator interaction opposes binding by ∼73kcal/mol at physiological salt concentrations and neutral pH. A variety of entropic terms also oppose binding. The major force driving the binding process appears to be release of interfacial water from the protein and DNA surfaces upon complexation and, possibly, enhanced packing interactions between the protein and DNA in the interface. When the various nonelectrostatic terms are described with simple models that have been applied previously to other binding processes, a general picture of protein/DNA association emerges in which binding is driven by the nonpolar interactions, whereas specificity results from electrostatic interactions that weaken binding but are necessary components of any protein/DNA complex.

Electrostatic effects on protein stability: Current Opinion in Structural Biology 1992, 2:40…-45

Abstract Recent experimental and theoretical studies have led to new insights into the contribution of ionizable amino acids to protein stability. The role of polar groups is less clear, in part because their interactions are difficult to control experimentally.

Protein backbone angle prediction with machine learning approaches

MOTIVATION Protein backbone torsion angle prediction provides useful local structural information that goes beyond conventional three-state (alpha, beta and coil) secondary structure predictions. Accurate prediction of protein backbone torsion angles will substantially improve modeling procedures for local structures of protein sequence segments, especially in modeling loop conformations that do not form regular structures as in alpha-helices or beta-strands. RESULTS We have devised two novel automated methods in protein backbone conformational state prediction: one method is based on support vector machines (SVMs); the other method combines a standard feed-forward back-propagation artificial neural network (NN) with a local structure-based sequence profile database (LSBSP1). Extensive benchmark experiments demonstrate that both methods have improved the prediction accuracy rate over the previously published methods for conformation state prediction when using an alphabet of three or four states. AVAILABILITY LSBSP1 and the NN algorithm have been implemented in PrISM.1, which is available from www.columbia.edu/~ay1/. SUPPLEMENTARY INFORMATION Supplementary data for the SVM method can be downloaded from the Website www.cs.columbia.edu/compbio/backbone.

SEQUENCE TO STRUCTURE ALIGNMENT IN COMPARATIVE MODELING USING PRISM

PrISM (Protein Informatics System for Modeling) is a protein analysis and modeling system in which informatics, alignment, modeling, and assessment modules are integrated in a computational environment where protein analysis and modeling protocols can be designed and assessed interactively. It can then be used automatically and repetitively in response to a variety of protein analysis and modeling problems. PrISM was used to predict a single model for each of the 43 targets in the CASP3 experiment. In this paper, we present results for 13 target sequences, which we consider to be comparative modeling targets with clearly related structural templates. We emphasize the problem of aligning a target sequence to a template structure with various alignment methods. When more than one alignment method and/or parameter set are applied, the final alignment is chosen on the basis of a model ranking system also used in PrISMs fold recognition module. Advanced sequence–template alignment procedures in PrISM are useful in some cases when standard pairwise dynamic programming algorithm fail to make any reasonable global alignment. The same procedures, however, failed in other cases, corresponding to remotely related query‐template pairs that involved extensive insertions and deletions. Proteins Suppl 1999;3:66–72.

A Practical Synthesis of Zanamivir Phosphonate Congeners with Potent Anti-influenza Activity

Two phosphonate compounds 1a (4-amino-1-phosphono-DANA) and 1b (phosphono-zanamivir) are synthesized and shown more potent than zanamivir against the neuraminidases of avian and human influenza viruses, including the oseltamivir-resistant strains. For the first time, the practical synthesis of these phosphonate compounds is realized by conversion of sialic acid to peracetylated phosphono-DANA diethyl ester (5) as a key intermediate in three steps by a novel approach. In comparison with zanamivir, the high affinity of 1a and 1b can be partly attributable to the strong electrostatic interactions of their phosphonate groups with the three arginine residues (Arg118, Arg292, and Arg371) in the active site of neuraminidases. These phosphonates are nontoxic to the human 293T cells; they protect cells from influenza virus infection with EC(50) values in low-nanomolar range, including the wild-type WSN (H1N1), the 2009 pandemic (H1N1), the oseltamivir-resistant H274Y (H1N1), RG14 (H5N1), and Udorn (H3N2) influenza strains.