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Archives of Biochemistry and Biophysics 602 (2016) 1e2

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Archives of Biochemistry and Biophysics


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Editorial

Macromolecular crystallography: An old science with new perspectives*

Since 1934, the year when John Bernal and Dorothy Crowfoot last three years. The fast development of new synchrotron light fa-
took the rst diffraction pattern from a protein crystal, macromo- cilities is key to this rapid growth. Since the rst measurements of a
lecular crystallography has come a long way. This milestone opened protein in a synchrotron facility, performed in the 1970's, synchro-
the door to the protein-structure age, but also revealed that some tron macromolecular crystallography beamlines have improved in
other problems had to be solved before getting to know protein many aspects. These include optical components, end-station
structures, among then the well-known phase-problem. In this design, sample delivery, visualization and positioning, sample envi-
long distance-race to success, it took more than 20 years to solve ronment, beam shaping, detectors and data acquisition, and pro-
the rst crystal structure, when John Kendrew and Max Perutz cessing software. Details from these aspects of the
determined the myoglobin's structure [1]. This landmark was instrumentation that nowadays allow fast data collection and pro-
feasible thanks to the effort and hard work of the most brilliant sci- cessing at synchrotron facilities are compiled in the article Current
entic minds of the XXth century. Many of them were honoured advances in synchrotron radiation instrumentation for MX experi-
with the Nobel Prize award, others died before being ofcially ments in this issue by Jordi Juanhuix et al. [4].
recognized. Although important milestones in macromolecular crystallog-
Today, obtaining 3D models of biological macromolecules by raphy have been accomplished, there are still some frontiers. Not
means of X-ray diffraction has become much easier, and macromo- all proteins produce well diffracting crystals, especially membrane
lecular crystallographers are facing new challenges. In this special proteins. Most of the time, these proteins produce small and poorly
issue we have tried to give a snapshot of the state of art of macro- ordered crystals of reduced quality, hampering structural determi-
molecular crystallography through several reviews devoted to nation. Nowadays, a revolution in the macromolecular crystallog-
different facets of the eld. As all crystallographic structures begin raphy eld is taking place with the advent of new X-ray free
with their crystals, we initiated this volume with the article Current electron lasers (XFEL) and their implementation in serial femto-
trends in protein crystallization by Jose A. Gavira [2]. Protein crystal- second crystallography (SFX). Petra Fromme et al. analyze the
lization, once the bottleneck of the protein crystallography, is now most recent advances in these techniques in the article Serial
undergoing rapid development through the introduction of new Femtosecond Crystallography: a revolution in structural biology [5].
techniques that allow one to obtain crystals from almost any pro- For many years, the main criticism of crystallography has been its
tein. Unfortunately, there is no rule to tell us the crystallization con- static view of proteins, but now SFX is opening a new avenue of ex-
ditions of a protein from just its chemical composition; therefore, periments to record molecular movies of catalytic reactions. This
crystallizing proteins remains a trial and error procedure. Never- technique affords a new opportunity to obtain crystal structures of
theless, several attempts to rationalize this process have been poorly diffracting crystals such as those of membrane proteins.
made and these are described in the article Computational crystalli- These proteins do not produce large crystals, but many times
zation by Edward Snell et al. [3]. Today, several databases facilitate they produce well diffracting nanocrystals, which are ideal for
the crystallographer's work by giving advice on the most promising time-resolve studies. For efcient SFX it is important to determine
conditions to crystallize a protein. These predictions have become sample monodispersity and lattice quality of nanocrystals. Trans-
better as the number of protein structures available gives us more mission electron microscopy (TEM) is a valuable technique to deter-
information on the successful crystallization conditions for individ- mine these parameters and an example is reported in the article
ual proteins. Unfortunately, valuable information is lost as such da- Assessment of microcrystal quality by transmission electron micro-
tabases do not compile failed conditions. Therefore, any scopy for efcient serial femtosecond crystallography by Guillermo
computational analysis of protein crystallization requires complete Calero et al. [6]. Still, some proteins cannot be crystallized by any
and correctly formatted data. means and techniques such as small angle X-ray scattering
Since the Protein Data Bank (PDB) was funded in 1971, more (SAXS) have become essential to obtain structural information in
than 100 thousand protein structural models have been deposited. solution. Furthermore, SAXS experiments give relevant information
As we are writing this short editorial note, there are about 120 about aggregation processes in solution. Recent developments and
thousand structures, and 25% of them have been deposited in the future perspectives on BioSAXS are compiled by Bente Vestergaard
in her article Analysis of biostructural changes, dynamics, and interac-
tions: Small angle X-ray scattering to the rescue [7].
*
This article is part of a Special Issue entitled Protein Crystallography, edited by One of the mayor difculties to obtaining the crystal structure of
Ana Camara-Artigas and Jose Antonio Gavira.

http://dx.doi.org/10.1016/j.abb.2016.05.004
0003-9861/ 2016 Elsevier Inc. All rights reserved.
2 Editorial / Archives of Biochemistry and Biophysics 602 (2016) 1e2

a protein is that the information about the phase is lost in the indi- drugs [10].
vidual reections recorded in the X-ray diffraction images, so that Finally, to close this special issue, as protein crystallography has
phasing is the second classical bottleneck in protein crystallog- been used to understand protein structure-function relationship, it
raphy. As we mentioned before, it took many years to solve this can also be an invaluable tool in understanding the determinants of
difcult problem; its solution was nally reached by introducing protein misfolding. Crystallographic studies on protein misfolding:
heavy atoms into the protein crystals. This approach was rst domain swapping and amyloid formation in the SH3 domain by
applied by Dorothy Crowfoot to obtain the complex structure of Camara-Artigas describes how structural information obtained by
vitamin B12 and afterward for many years it was systematically means of crystal structures that suffer 3D domain-swapping can
applied to determine many protein structures. Nowadays, as the help to decipher the initial steps of another important protein
number of known protein structures grows, molecular replacement misfolding process, amyloid formation [11].
has become the favourite technique to obtain phases, but some pro-
tein structures still cannot be solved by this procedure. Here is
where single wavelength anomalous diffraction (SAD) techniques References
offer unique features to solve the phase problem. SAD phasing: his-
[1] H.F. Judson, The Eight Day of Creation. Makers of the Revolution in Biology,
tory, current impact and future opportunities by Bi-Cheng Wang et al.
Cold Spring Harbor Laboratory Press, 1996.
describes the actual development of this technique which is appli- [2] J.A. Gavira, Arch. Biochem. Biophys.
cable to proteins as large as 266 kDa, such as the T2R-TTL multi- [3] I. Altan, P. Charbonneau, E.H. Snell, Arch. Biochem. Biophys.
[4] R.L. Owen, J. Juanhuix, M. Fuchs, Arch. Biochem. Biophys.
protein complex [8].
[5] J.M.C. Martin-Garcia, C. Coe, J. Roy-Chowdhury, S. Fromme, Arch. Biochem.
Macromolecular crystallography is not the end but the means. Biophys.
For this reason, to complete this issue we have also included a [6] C.O. Barnes, E.G. Kovaleva, X. Fu, H.P. Stevenson, A.S. Brewster, D.P. DePonte,
few examples of how macromolecular crystallography is an invalu- E.L. Baxter, A.E. Cohen, G. Calero, Arch. Biochem. Biophys.
[7] B. Vestergaard, Arch. Biochem. Biophys.
able tool to unveil the secrets of proteins and nucleic acids. Since [8] J.P. Rose, B.C. Wang, Arch. Biochem. Biophys.
the rst photographs of the diffraction pattern of DNA were taken [9] P. Fernandez-Millan, C. Schelcher, J. Chihade, B. Masquida, P. Giege, C. Sauter,
by Rosalind Franklin, which allowed Watson and Crick to propose Arch. Biochem. Biophys.
[10] G. Di Nardo, V. Dell'Angelo, G. Catucci, S.J. Sadeghi, G. Gilardi, Arch. Biochem.
their double helix model, many secrets of these macromolecules Biophys.
have been unveiled by X-ray diffraction of crystals containing [11] A. Camara-Artigas, Arch. Biochem. Biophys.
nucleic acids alone or in complexes with proteins. Although the
rst crystal structure of a tRNA was determined forty years ago, Ana Ca mara-Artigas*
there are still many secrets to be revealed. The history and recent Dpt. Chemistry and Physics, Universidad de Almeria, CEIA3, Carretera
advances in the eld are compiled in the review Transfer RNA: Sacramento s/n, 04120 Almeria, Spain
from pioneering crystallographic studies to contemporary tRNA
biology by Claude Sauter et al. [9].  Antonio Gavira
Jose
Crystallography is a priceless tool for many elds, but especially Laboratory for Crystallographic Studies, Instituto Andaluz de Ciencias
for enzymology. The availability of the structures of enzymes in the de la Tierra, CSIC-UGR, Avd. Las Palmeras, 4, E-18100, Armilla, Spain
presence of different ligands has denitively helped us to under- E-mail addresses: jgavira@iact.ugr-csic.es, http://www.lec.csic.es/
stand enzymes' catalytic behaviour and their regulation through gavi/.
the binding of small molecules. This knowledge is needed for the
*
development and improvement of drugs. The article Subtle struc- Corresponding author.
tural changes in the Asp251Gly/Gln307His P450 BM3 mutant respon- E-mail addresses: acamara@ual.es, http://www.ual.es/personal/
sible for new activity toward diclofenac, tolbutamide and ibuprofen by acamara (A. Camara-Artigas).
Gianfranco Gilardi et al. is an example of how this information can
be obtained and how it can produce key information to improve Available online 6 May 2016