The parallel and synergistic developments of atomic resolution structural information, new spectroscopic methods, their underpinning formalism, and the application of sophisticated theoretical methods have led to a step function change in our understanding of photosynthetic light harvesting, the process by which photosynthetic organisms collect solar energy and supply it to their reaction centers to initiate the chemistry of photosynthesis. The new spectroscopic methods, in particular multidimensional spectroscopies, have enabled a transition from recording rates of processes to focusing on mechanism. We discuss two ultrafast spectroscopies – two-dimensional electronic spectroscopy and two-dimensional electronic-vibrational spectroscopy – and illustrate their development through the lens of photosynthetic light harvesting. Both spectroscopies provide enhanced spectral resolution and, in different ways, reveal pathways of energy flow and coherent oscillations which relate to the quantum mechanical mixing of, for example, electronic excitations (excitons) and nuclear motions. The new types of information present in these spectra provoked the application of sophisticated quantum dynamical theories to describe the temporal evolution of the spectra and provide new questions for experimental investigation. While multidimensional spectroscopies have applications in many other areas of science, we feel that the investigation of photosynthetic light harvesting has had the largest influence on the development of spectroscopic and theoretical methods for the study of quantum dynamics in biology, hence the focus of this review. We conclude with key questions for the next decade of this review.

In this issue, we introduce a new format. To meet reader demand, QRB will augment its long-standing commitment to Reviews with Essays. Essays will be brief, timely commentaries considering one or more of the following: a new idea, a new argument about an old idea, the answer to an outstanding question, a new method, a new interpretation, or a subject otherwise of importance to biophysicists. Whereas Reviews are intellectually rigorous reports that stand as definitive statements on a subject for many years, Essays will seek to apply the same high standard to highlighting a moment in time, to show us where we stand and, so, to infer our trajectory. Essays will appear as deemed appropriate; this inaugural year will be replete with an Essay each quarter. The Board is pleased to announce that our Essayists for 2004 will be Richard Henderson (this issue), Donald Crothers (May), Christopher Miller (August) and Brian Matthews (November).

The Nobel Workshop ‘Fundamentals of Biomolecular Function: Nucleic Acids, Proteins, and Membranes’, was hosted by the city of Coimbra, Portugal, and the University of Coimbra in May 2005. The workshop focused on three subjects: (i) the functions of biological macromolecules, (ii) the interactions underlying these functions, and (iii) new techniques for studying these interactions. A brief summary of the discussions follows.

RecA family proteins pair two DNAs with the same sequence to promote strand exchange during homologous recombination. To understand how RecA proteins search for and recognize homology, we sought to determine the length of homologous sequence that permits RecA to start its reaction. Specifically, we analyzed the effect of sequence heterogeneity on the association rate of homologous DNA with RecA/single-stranded DNA complex. We assumed that the reaction can start with equal likelihood at any point in the DNA, and that sequence heterogeneity abolishes some possible initiation sites. This analysis revealed that the effective recognition size is five or six nucleotides, larger than the three nucleotides recognized by a RecA monomer. Because the first DNA is elongated 1.5-fold by intercalation of amino acid residues of RecA every three bases, the second bound DNA must be elongated to pair with the first. Because this length is similar to estimates based on the strand-exchange reaction or DNA pair formation, the homology test is likely to occur primarily at the association step. The energetic difference due to the absence of hydrogen bonding is too small to discriminate single-nucleotide heterogeneity over a five- or six-nucleotide sequence. The selection is very likely to be made kinetically, and probably involves some structural factor other than Watson–Crick hydrogen bonding. It would be valuable to determine whether this is also the case for other biological reactions involving DNA base complementarity, such as replication, transcription, and translation.

Max Ferdinand Perutz, molecular biologist; born Vienna 19 May 1914; Director, MRC Unit for Molecular Biology 1947–62; FRS 1954; Reader, Davy Faraday Research Laboratory, Royal Institution 1954–68, Fullerian Professor of Physiology 1973–79; Chairman, MRC Laboratory of Molecular Biology 1962–79; Nobel Prize for Chemistry (jointly) 1962; CBE 1963; Chairman, European Molecular Biology Organisation 1963–69; CH 1975; OM 1988; married 1942 Gisela Peiser (one son, one daughter); died Cambridge 6 February 2002.

Among the different fields of natural sciences, physics is concerned with the most basic properties of matter. It is possible to define the necessary physical concepts in a rather unique way and carry out experiments under well-controlled conditions. The interpretation of experiments is therefore comparatively easy. In chemistry the situation is more complicated and the interpretation becomes more ambiguous. Biology finally is characterized by its high degree of complexity, making the detailed analysis difficult. Since the problems of biology are so essential, it is very important to use every tool available to clarify the situation, state the problems as carefully as possible and approximate the solution from as many sides as are feasible. Therefore, not only the methods developed within biology but also those pertinent to chemistry and physics should be applied. For this reason also quantum mechanics may be able to contribute to the elucidation of biological problems.

Although viral protein structure and replication mechanisms have been explored extensively with X-ray crystallography, cryo-electron microscopy, and population imaging studies, these methods are often not able to distinguish dynamic conformational changes in real time. Single-molecule fluorescence resonance energy transfer (smFRET) offers unique insights into interactions and states that may be missed in ensemble studies, such as nucleic acid or protein structure, and conformational transitions during folding, receptor–ligand interactions, and fusion. We discuss the application of smFRET to the study of viral protein conformational dynamics, with a particular focus on viral glycoprotein dynamics, viral helicases, proteins involved in HIV reverse transcription, and the influenza RNA polymerase. smFRET experiments have played a crucial role in deciphering conformational changes in these processes, emphasising the importance of smFRET as a tool to help elucidate the life cycle of viral pathogens and identify key anti-viral targets.

Large scale functional motions of molecules are studied experimentally using numerous molecular and biophysics techniques, the data from which are subsequently interpreted using diverse models of Brownian molecular dynamics. To unify all rotational physics techniques and motional models, the frame order tensor – a universal statistical mechanics theory based on the rotational ordering of rigid body frames – is herein formulated. The frame ordering is the fundamental physics that governs how motions modulate rotational molecular physics and it defines the properties and maximum information content encoded in the observable physics. Using the tensor to link residual dipolar couplings and pseudo-contact shifts, two distinct information-rich and atomic-level biophysical measurements from the field of nuclear magnetic resonance spectroscopy, to a number of basic mechanical joint models, a highly dynamic state of calmodulin (CaM) bound to a target peptide in a tightly closed conformation was observed. Intra- and inter-domain motions reveal the CaM complex to be entropically primed for peptide release.

Volume 37 Number 2 (May 2004), pp. 147–195

Cell-penetrating peptides: from inception to application

Due to a correction error at the Press stage the title of this paper was incorrectly published with the word ‘small’ included. The correct title is given above.

The publisher apologizes to the authors and readers for this error.

Structure-switching aptamers have become ubiquitous in several applications, notably in analytical devices such as biosensors, due to their ease of supporting strong signaling. Aside from their ability to bind specifically with their respective target, this class of aptamers also undergoes a conformational rearrangement upon target recognition. While several well-studied and early-developed aptamers (e.g., cocaine, ATP, and thrombin) have been found to have this structure-switching property, the vast majority do not. As a result, it is common to try to engineer aptamers into switches. This proves challenging in part because of the difficulty in obtaining structural and functional information about aptamers. In response, we review various readily available biophysical characterization tools that are capable of assessing structure switching of aptamers. In doing so, we delve into the fundamentals of these different techniques and detail how they have been utilized in characterizing structure-switching aptamers. While each of these biophysical techniques alone has utility, their real power to demonstrate the occurrence of structural change with ligand binding is when multiple techniques are used. We hope that through a deeper understanding of these techniques, researchers will be better able to acquire biophysical information about their aptamer–ligand systems and accelerate the translation of aptamers into biosensors.

Molecular motors are machines essential for life since they convert chemical energy into mechanical work. However, the precise mechanism by which nucleotide binding, catalysis, or release of products is coupled to the work performed by the molecular motor is still not entirely clear. This is due, in part, to a lack of understanding of the role of force in the mechanical–structural processes involved in enzyme catalysis. From a mechanical perspective, one promising hypothesis is the Haldane–Pauling hypothesis which considers the idea that part of the enzymatic catalysis is strain-induced. It suggests that enzymes cannot be efficient catalysts if they are fully complementary to the substrates. Instead, they must exert strain on the substrate upon binding, using enzyme-substrate energy interaction (binding energy) to accelerate the reaction rate. A novel idea suggests that during catalysis, significant strain energy is built up, which is then released by a local unfolding/refolding event known as ‘cracking’. Recent evidence has also shown that in catalytic reactions involving conformational changes, part of the heat released results in a center-of-mass acceleration of the enzyme, raising the possibility that the heat released by the reaction itself could affect the enzyme’s integrity. Thus, it has been suggested that this released heat could promote or be linked to the cracking seen in proteins such as adenylate kinase (AK). We propose that the energy released as a consequence of ligand binding/catalysis is associated with the local unfolding/refolding events (cracking), and that this energy is capable of driving the mechanical work.

Yeast frataxin (Yfh1) is a small natural protein from yeast that has the unusual property of undergoing cold denaturation at temperatures above the freezing point of water when under conditions of low ionic strength. This peculiarity, together with remarkable resilience, allows the determination, for the whole protein as well as for individual residues, of the stability curve, that is the temperature dependence of the free energy difference between the unfolded and folded forms. The ease of measuring stability curves without the need to add denaturants or introduce ad hoc destabilizing mutations makes this protein an ideal ‘tool’ for investigating the influence of many environmental factors on protein stability. The present review aims at recapitulating all the open questions that Yfh1 has helped to address, including understanding the differences and commonalities of the cold, heat and pressure unfolded states. This protein thus offers a unique tool for studying aspects of protein stability so far been considered difficult to assess and provides important guidelines that could allow the identification of other similar systems.

Zoonoses are infectious agents that are transmissible between animals and humans. Up to 60% of known infectious diseases and 75% of emergent diseases are zoonotic. Genomic variation between homeostatic populations provides a novel window into the effect of environmental pathogens on allelic distributions within the populations. Genodynamics is a biophysical approach utilizing developed metrics on biallelic single-nucleotide polymorphisms (SNPs) that can be used to quantify the adaptive influences due to pathogens. A genomic free energy that is minimized when overall population health is optimized describes the influence of environmental agents upon genomic variation. A double-blind exploration of over 100 thousand SNPs searching for smooth functional dependencies upon four zoonotic pathogens carried by four possible hosts amidst populations that live in their ancestral environments has been conducted. Exemplars that infectious agents can have significant adaptive influence on human populations are presented. One discussed SNP is likely associated with both adaptive and innate immune regulation. The adaptive response of another SNP suggests an intriguing connection between zoonoses and human cancers. The adaptive forces of the presented pathogens upon the human genome have been quantified.

Exposure to various chemicals, either due to occupation or lifestyle, is considered to be a major contributing factor to tumour formation in man (Higginson, 1969; Doll & Peto, 1981). An important and prevalent class of potent carcinogenic compounds present in the environment is polycyclic aromatic hydrocarbons (PAHs), which are found in various petroleum and combustion products derived from heat and power generation and motor vehicle exhausts (Baum, 1978). Furthermore, since PAHs are generally formed by pyrolysis of organic matters such as tobacco smoking and certain procedures of food preparation, the PAH exposure to humans is extensive.

In the very short time since magnetic resonance imaging (MRI) was born it has gained surprisingly rapid and enthusiastic acceptance and has speedily proliferated, particularly in the United States and Western Europe. Magnetic resonance imaging (MRI) has successfully challenged computed tomography (CT) in all areas of the body where respiratory motion does not degrade the image (Steinberg, 1986). Newer techniques using a multiplicity of approaches are starting to close the gap between CT and MRI, even in the upper abdomen where the effects of respiratory motion are most pronounced. Although MR is already widely clinically applied and is an accepted everyday diagnostic modality in most large medical centres in the United States, it is not a mature modality. It is rapidly evolving, with whole new areas opening to investigation which will vastly broaden its applications.