Archives of Biochemistry and Biophysics 602 (2016) 1e2
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Editorial
Macromolecular crystallography: An old science with new perspectives*
Since 1934, the year when John Bernal and Dorothy Crowfoot
took the rst diffraction pattern from a protein crystal, macromo-
lecular crystallography has come a long way. This milestone opened
the door to the protein-structure age, but also revealed that some
other problems had to be solved before getting to know protein
structures, among then the well-known phase-problem. In this
long distance-race to success, it took more than 20 years to solve
the rst crystal structure, when John Kendrew and Max Perutz
determined the myoglobin's structure [1]. This landmark was
feasible thanks to the effort and hard work of the most brilliant sci-
entic minds of the XXth century. Many of them were honoured
with the Nobel Prize award, others died before being ofcially
recognized.
Today, obtaining 3D models of biological macromolecules by
means of X-ray diffraction has become much easier, and macromo-
lecular crystallographers are facing new challenges. In this special
issue we have tried to give a snapshot of the state of art of macro-
molecular crystallography through several reviews devoted to
different facets of the eld. As all crystallographic structures begin
with their crystals, we initiated this volume with the article Current
trends in protein crystallization by Jose A. Gavira [2]. Protein crystal-
lization, once the bottleneck of the protein crystallography, is now
undergoing rapid development through the introduction of new
techniques that allow one to obtain crystals from almost any pro-
tein. Unfortunately, there is no rule to tell us the crystallization con-
ditions of a protein from just its chemical composition; therefore,
crystallizing proteins remains a trial and error procedure. Never-
theless, several attempts to rationalize this process have been
made and these are described in the article Computational crystalli-
zation by Edward Snell et al. [3]. Today, several databases facilitate
the crystallographer's work by giving advice on the most promising
conditions to crystallize a protein. These predictions have become
better as the number of protein structures available gives us more
information on the successful crystallization conditions for individ-
ual proteins. Unfortunately, valuable information is lost as such da-
tabases do not compile failed conditions. Therefore, any
computational analysis of protein crystallization requires complete
and correctly formatted data.
Since the Protein Data Bank (PDB) was funded in 1971, more
than 100 thousand protein structural models have been deposited.
As we are writing this short editorial note, there are about 120
thousand structures, and 25% of them have been deposited in the
*
This article is part of a Special Issue entitled Protein Crystallography, edited by
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.
last three years. The fast development of new synchrotron light fa-
cilities is key to this rapid growth. Since the rst measurements of a
protein in a synchrotron facility, performed in the 1970's, synchro-
tron macromolecular crystallography beamlines have improved in
many aspects. These include optical components, end-station
design, sample delivery, visualization and positioning, sample envi-
ronment, beam shaping, detectors and data acquisition, and pro-
cessing software. Details from these aspects of the
instrumentation that nowadays allow fast data collection and pro-
cessing at synchrotron facilities are compiled in the article Current
advances in synchrotron radiation instrumentation for MX experi-
ments in this issue by Jordi Juanhuix et al. [4].
Although important milestones in macromolecular crystallog-
raphy have been accomplished, there are still some frontiers. Not
all proteins produce well diffracting crystals, especially membrane
proteins. Most of the time, these proteins produce small and poorly
ordered crystals of reduced quality, hampering structural determi-
nation. Nowadays, a revolution in the macromolecular crystallog-
raphy eld is taking place with the advent of new X-ray free
electron lasers (XFEL) and their implementation in serial femto-
second crystallography (SFX). Petra Fromme et al. analyze the
most recent advances in these techniques in the article Serial
Femtosecond Crystallography: a revolution in structural biology [5].
For many years, the main criticism of crystallography has been its
static view of proteins, but now SFX is opening a new avenue of ex-
periments to record molecular movies of catalytic reactions. This
technique affords a new opportunity to obtain crystal structures of
poorly diffracting crystals such as those of membrane proteins.
These proteins do not produce large crystals, but many times
they produce well diffracting nanocrystals, which are ideal for
time-resolve studies. For efcient SFX it is important to determine
sample monodispersity and lattice quality of nanocrystals. Trans-
mission electron microscopy (TEM) is a valuable technique to deter-
mine these parameters and an example is reported in the article
Assessment of microcrystal quality by transmission electron micro-
scopy for efcient serial femtosecond crystallography by Guillermo
Calero et al. [6]. Still, some proteins cannot be crystallized by any
means and techniques such as small angle X-ray scattering
(SAXS) have become essential to obtain structural information in
solution. Furthermore, SAXS experiments give relevant information
about aggregation processes in solution. Recent developments and
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].
One of the mayor difculties to obtaining the crystal structure of
2 Editorial / Archives of Biochemistry and Biophysics 602 (2016) 1e2
a protein is that the information about the phase is lost in the indi-
vidual reections recorded in the X-ray diffraction images, so that
phasing is the second classical bottleneck in protein crystallog-
raphy. As we mentioned before, it took many years to solve this
difcult problem; its solution was nally reached by introducing
heavy atoms into the protein crystals. This approach was rst
applied by Dorothy Crowfoot to obtain the complex structure of
vitamin B12 and afterward for many years it was systematically
applied to determine many protein structures. Nowadays, as the
number of known protein structures grows, molecular replacement
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
offer unique features to solve the phase problem. SAD phasing: his-
tory, current impact and future opportunities by Bi-Cheng Wang et al.
describes the actual development of this technique which is appli-
cable to proteins as large as 266 kDa, such as the T2R-TTL multi-
protein complex [8].
Macromolecular crystallography is not the end but the means.
For this reason, to complete this issue we have also included a
few examples of how macromolecular crystallography is an invalu-
able tool to unveil the secrets of proteins and nucleic acids. Since
the rst photographs of the diffraction pattern of DNA were taken
by Rosalind Franklin, which allowed Watson and Crick to propose
their double helix model, many secrets of these macromolecules
have been unveiled by X-ray diffraction of crystals containing
nucleic acids alone or in complexes with proteins. Although the
rst crystal structure of a tRNA was determined forty years ago,
there are still many secrets to be revealed. The history and recent
advances in the eld are compiled in the review Transfer RNA:
from pioneering crystallographic studies to contemporary tRNA
biology by Claude Sauter et al. [9].
Crystallography is a priceless tool for many elds, but especially
for enzymology. The availability of the structures of enzymes in the
presence of different ligands has denitively helped us to under-
stand enzymes' catalytic behaviour and their regulation through
the binding of small molecules. This knowledge is needed for the
development and improvement of drugs. The article Subtle struc-
tural changes in the Asp251Gly/Gln307His P450 BM3 mutant respon-
sible for new activity toward diclofenac, tolbutamide and ibuprofen by
Gianfranco Gilardi et al. is an example of how this information can
be obtained and how it can produce key information to improve
drugs [10].
Finally, to close this special issue, as protein crystallography has
been used to understand protein structure-function relationship, it
can also be an invaluable tool in understanding the determinants of
protein misfolding. Crystallographic studies on protein misfolding:
domain swapping and amyloid formation in the SH3 domain by
Camara-Artigas describes how structural information obtained by
means of crystal structures that suffer 3D domain-swapping can
help to decipher the initial steps of another important protein
misfolding process, amyloid formation [11].
References
[1] H.F. Judson, The Eight Day of Creation. Makers of the Revolution in Biology,
Cold Spring Harbor Laboratory Press, 1996.
[2] J.A. Gavira, Arch. Biochem. Biophys.
[3] I. Altan, P. Charbonneau, E.H. Snell, Arch. Biochem. Biophys.
[4] R.L. Owen, J. Juanhuix, M. Fuchs, Arch. Biochem. Biophys.
[5] J.M.C. Martin-Garcia, C. Coe, J. Roy-Chowdhury, S. Fromme, Arch. Biochem.
Biophys.
[6] C.O. Barnes, E.G. Kovaleva, X. Fu, H.P. Stevenson, A.S. Brewster, D.P. DePonte,
E.L. Baxter, A.E. Cohen, G. Calero, Arch. Biochem. Biophys.
[7] B. Vestergaard, Arch. Biochem. Biophys.
[8] J.P. Rose, B.C. Wang, Arch. Biochem. Biophys.
[9] P. Fernandez-Millan, C. Schelcher, J. Chihade, B. Masquida, P. Giege, C. Sauter,
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[10] G. Di Nardo, V. Dell'Angelo, G. Catucci, S.J. Sadeghi, G. Gilardi, Arch. Biochem.
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[11] A. Camara-Artigas, Arch. Biochem. Biophys.
Ana Ca mara-Artigas*
Dpt. Chemistry and Physics, Universidad de Almeria, CEIA3, Carretera
Sacramento s/n, 04120 Almeria, Spain
 Antonio Gavira
Jose
Laboratory for Crystallographic Studies, Instituto Andaluz de Ciencias
de la Tierra, CSIC-UGR, Avd. Las Palmeras, 4, E-18100, Armilla, Spain
E-mail addresses: jgavira@iact.ugr-csic.es, http://www.lec.csic.es/
gavi/.
*
Corresponding author.
E-mail addresses: acamara@ual.es, http://www.ual.es/personal/
acamara (A. Camara-Artigas).
Available online 6 May 2016